` contains the exact IRIDA version this plugin will need to be compiled against (compile-time version).
+
+## 5. Build and Test
+
+Once you've made all the updates, you can try building and testing your plugin. To build your plugin, you can run:
+
+```bash
+mvn clean package
+```
+
+You should find your packaged plugin JAR file in `target/` (e.g., `target/example-plugin-0.1.0-SNAPSHOT.jar`).
+
+To test out this plugin, please copy to `/etc/irida/plugins` on a machine with IRIDA installed and restart IRIDA. Your plugin should show up in the **Analyses > Pipelines** page in IRIDA.
+
+![example-plugin-pipeline.png][]
+
+You should also be able to see messages like below in the IRIDA log file when starting up:
+
+```
+INFO org.pf4j.AbstractPluginManager:801 - Plugin 'example-plugin@0.1.0' resolved
+INFO org.pf4j.AbstractPluginManager:320 - Start plugin 'example-plugin@0.1.0'
+DEBUG ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig:45 - Loaded 1 valid pipeline plugins.
+```
+
+## 6. Distribute
+
+Once you've successfully built your plugin, you can distribute the JAR file to other IRIDA users to install in their instances.
+
+[maven]: https://maven.apache.org/
+[IRIDA]: http://irida.ca/
+[Galaxy]: https://galaxyproject.org/
+[Java]: https://www.java.com/
+[irida-pipeline]: https://irida.corefacility.ca/documentation/developer/tools/pipelines/
+[irida-pipeline-galaxy]: https://irida.corefacility.ca/documentation/developer/tools/pipelines/#galaxy-workflow-development
+[irida-wf-ga2xml]: https://github.com/phac-nml/irida-wf-ga2xml
+[pom.xml]: pom.xml
+[workflows-dir]: src/main/resources/workflows
+[workflow-structure]: src/main/resources/workflows/0.1.0/irida_workflow_structure.ga
+[example-plugin-java]: src/main/java/ca/corefacility/bioinformatics/irida/plugins/ExamplePlugin.java
+[irida-plugin-java]: https://github.com/phac-nml/irida/tree/development/src/main/java/ca/corefacility/bioinformatics/irida/plugins/IridaPlugin.java
+[irida-updater]: src/main/java/ca/corefacility/bioinformatics/irida/plugins/ExamplePluginUpdater.java
+[irida-setup]: https://irida.corefacility.ca/documentation/administrator/index.html
+[properties]: https://en.wikipedia.org/wiki/.properties
+[messages]: src/main/resources/workflows/0.1.0/messages_en.properties
+[maven-min-pom]: https://maven.apache.org/guides/introduction/introduction-to-the-pom.html#Minimal_POM
+[pf4j-start]: https://pf4j.org/doc/getting-started.html
+[example-plugin-results.png]: doc/images/example-plugin-results.png
+[example-plugin-pipeline.png]: doc/images/example-plugin-pipeline.png
+[example-plugin-metadata.png]: doc/images/example-plugin-metadata.png
+[pipeline-parameters.png]: doc/images/pipeline-parameters.png
+[example-plugin-save-results.png]: doc/images/example-plugin-save-results.png
diff --git a/doc/images/example-plugin-metadata.png b/doc/images/example-plugin-metadata.png
new file mode 100644
index 0000000..e34129b
Binary files /dev/null and b/doc/images/example-plugin-metadata.png differ
diff --git a/doc/images/example-plugin-pipeline.png b/doc/images/example-plugin-pipeline.png
new file mode 100644
index 0000000..6475b01
Binary files /dev/null and b/doc/images/example-plugin-pipeline.png differ
diff --git a/doc/images/example-plugin-results.png b/doc/images/example-plugin-results.png
new file mode 100644
index 0000000..a1c9e5a
Binary files /dev/null and b/doc/images/example-plugin-results.png differ
diff --git a/doc/images/example-plugin-save-results.png b/doc/images/example-plugin-save-results.png
new file mode 100644
index 0000000..20aa244
Binary files /dev/null and b/doc/images/example-plugin-save-results.png differ
diff --git a/doc/images/pipeline-parameters.png b/doc/images/pipeline-parameters.png
new file mode 100644
index 0000000..38f04c3
Binary files /dev/null and b/doc/images/pipeline-parameters.png differ
diff --git a/index-1.html b/index-1.html
new file mode 100644
index 0000000..7f90123
--- /dev/null
+++ b/index-1.html
@@ -0,0 +1,269 @@
+Unknown
+IRIDA Example Pipeline Plugin
+This project contains an example pipeline implemented as a plugin for the IRIDA bioinformatics analysis system. This can be used as a template for implementing your own pipelines within IRIDA. Please see the pipeline documentation at https://irida.corefacility.ca/documentation/developer/tools/pipelines/ for more details.
+Table of Contents
+
+Building/Packaging
+Building and packaging this code is accomplished using Apache Maven . However, you will first need to install IRIDA to your local Maven repository. The version of IRIDA you install will have to correspond to the version found in the irida.version.compiletime property in the pom.xml file of this project. Right now, this is IRIDA version 19.01.3.
+Installing IRIDA to local Maven repository
+To install IRIDA to your local Maven repository please do the following:
+
+Clone the IRIDA project
+
+bash
+git clone https://github.com/phac-nml/irida.git
+cd irida
+
+Checkout appropriate version of IRIDA
+
+bash
+git checkout 19.01.3
+
+Install IRIDA to local repository
+
+bash
+mvn clean install -DskipTests
+Building the plugin
+Once you've installed IRIDA as a dependency, you can proceed to building this plugin. Please run the following commands:
+```bash
+cd irida-plugin-example
+mvn clean package
+```
+Once complete, you should end up with a file target/example-plugin-1.0-SNAPSHOT.jar which can be installed as a plugin to IRIDA.
+If you have previously setup IRIDA before you may copy this JAR file to /etc/irida/plugins and restart IRIDA. The plugin should now show up in the Analyses > Pipelines section of IRIDA.
+
+You should be able to run a pipeline with this plugin and get analysis results.
+
+And, you should be able to save and view these results in the IRIDA metadata table.
+
+Dependencies
+The following dependencies are required in order to make use of this plugin.
+
+Using as a template for developing a plugin
+In order to use this project as a template for developing your own pluginable pipeline there are a few places you will need to change.
+
+The first set of files you will need to change are those under src/main/resources/workflows. The structure of this directory looks like:
+workflows/
+��������� 0.1.0
+ ��������� irida_workflow_structure.ga
+ ��������� irida_workflow.xml
+ ��������� messages_en.properties
+
+The directory 0.1.0 corresponds to all files for a particular version of a pipeline (in this case 0.1.0). Previous versions of the pipeline should each be kept in their own numbered directory (e.g., 0.1.0, 0.2.0) so that IRIDA can load up information about these pipelines.
+The file irida_workflow_structure.ga is a Galaxy workflow file which is uploaded to a Galaxy instance by IRIDA before execution.
+The file irida_workflow.xml contains information about this particular pipeline used by IRIDA.
+The file messages_en.properties contains messages which will be displayed in the IRIDA UI.
+
+Please replace any existing files in this directory using the following instructions.
+1.1. Creating pipeline files
+The necessary files that go under the workflows/ directory can be constructed manually (see the IRIDA Pipeline development documentation). However, an easier approach is to construct the files automatically using the irida-wf-ga2xml software and then customize the generated files.
+No matter which method you use (manually constructing the pipeline files, or automatically constructing them) you will need to start out by building your Galaxy workflow. Please follow the instructions in the IRIDA Pipelines documentation for how to do this. At the end, you should end up with a workflow.ga file exported from Galaxy, which is a JSON representation of your Galaxy workflow. Once you have this file (an example would be src/main/resources/workflows/0.1.0/irida_workflow_structure.ga ), you can run the following to automatically generate the other necessary files:
+bash
+java -jar irida-wf-ga2xml-1.0.0-SNAPSHOT-standalone.jar -n ReadInfo -t READ_INFO -W 0.1.0 -o output -i src/main/resources/workflows/0.1.0/irida_workflow_structure.ga
+The meaning of the command-line options are as follows:
+
+-n ReadInfo: The name of the pipeline, stored in the irida_workflow.xml file under <name>ReadInfo</name>.-t READ_INFO: The type of the pipeline, stored in the irida_workflow.xml file under <analysisType>READ_INFO</analysisType>. Corresponds to the AnalysisType object in the Java file listed above (ExamplePlugin.java ).-W 0.1.0: The version of the pipeline, stored in the irida_workflow.xml file under <version>0.1.0</version>.-o output: The directory to store all the output files.-i src/main/resources/workflows/0.1.0/irida_workflow_structure.ga: The input Galaxy workflow file.
+Once complete, the output files will be located under output/ and will look like:
+output/
+��������� ReadInfo
+ ��������� 0.1.0
+ ��������� irida_workflow_structure.ga
+ ��������� irida_workflow.xml
+ ��������� messages_en.properties
+You can directly move the 0.1.0 directory to src/main/resources/workflows.
+1.2. Updating pipeline files
+Once you've generated and moved your pipeline files to src/main/resources/workflows, you can make small adjustments to them as you see fit.
+1.2.1. Modifying irida_workflow.xml
+In particular, you may want to make adjustments to irida_workflow.xml to add/remove/change the parameters. These are stored in the XML file like:
+xml
+<parameters>
+ <parameter name="Grep1-4-invert" defaultValue="false">
+ <toolParameter toolId="Grep1" parameterName="invert"/>
+ </parameter>
+ <parameter name="Grep1-4-pattern" defaultValue="^@">
+ <toolParameter toolId="Grep1" parameterName="pattern"/>
+ </parameter>
+ <parameter name="wc_gnu-5-include_header" defaultValue="false">
+ <toolParameter toolId="wc_gnu" parameterName="include_header"/>
+ </parameter>
+</parameters>
+When loaded up in IRIDA, these will show up like:
+
+You may also wish to modify the particular output files that get saved by IRIDA. These are recorded in:
+xml
+<outputs>
+ <output name="hash.txt" fileName="hash.txt"/>
+ <output name="read-count.txt" fileName="read-count.txt"/>
+</outputs>
+The fileName attribute should correspond to a particular name of an output file in the *.ga workflow file (see irida_workflow_stucture.ga or the IRIDA Pipeline documentation for more details).
+1.2.2. Modifying messages_en.properties
+The file src/main/resources/workflows/0.1.0/messages_en.properties contains the text that gets displayed by IRIDA for the pipeline. The file is in the form of key = value entries (the Java .properties format). An example of this file would be:
+```properties
+pipeline.parameters.modal-title.readinfo=ReadInfo Pipeline Parameters
+workflow.READ_INFO.title=ReadInfo Pipeline
+pipeline.h1.ReadInfo=ReadInfo Pipeline
+pipeline.title.ReadInfo=Pipelines - ReadInfo
+workflow.READ_INFO.description=
+pipeline.parameters.readinfo.Grep1-4-invert=Grep1-4-invert
+pipeline.parameters.readinfo.Grep1-4-pattern=Grep1-4-pattern
+pipeline.parameters.readinfo.wc_gnu-5-include_header=wc_gnu-5-include_header
+```
+The entries like workflow.READ_INFO.title=ReadInfo Pipeline contain the text used to display the pipeline entry on the "Pipelines" page in the UI:
+
+The entries like pipeline.parameters.readinfo.Grep1-4-pattern=Grep1-4-pattern contain information used to display the text when adjusting pipeline parameters:
+
+The Grep1-4-pattern part corresponds to the name attribute under a <parameter> entry in the irida_workflow.xml file:
+xml
+<parameter name="Grep1-4-pattern" defaultValue="^@">
+ <toolParameter toolId="Grep1" parameterName="pattern"/>
+</parameter>
+
+This is the main class you will need to modify for your pipeline. The class can be located in any package you wish, and can have any name you wish. You will want to implement the two methods which are indicated as required in this file. You can also override the methods indicated as optional in the file for additional configuration. You should have a class looking like:
+```java
+public class ExamplePlugin extends Plugin {
+public static final AnalysisType MY_ANALYSIS_TYPE = new AnalysisType("MY_ANALYSIS_TYPE");
+
+public ExamplePlugin(PluginWrapper wrapper) {
+ super(wrapper);
+}
+
+@Extension
+public static class PluginInfo implements IridaPlugin {
+
+ /*** Required ***/
+
+ @Override
+ public AnalysisType getAnalysisType() {
+ return new AnalysisType("READ_INFO");
+ }
+
+ @Override
+ public UUID getDefaultWorkflowUUID() {
+ return UUID.fromString("79d90ca8-00ae-441b-b5c7-193c9e85a968");
+ }
+
+ /*** Optional ***/
+
+ @Override
+ public Optional<Color> getBackgroundColor() {
+ return Optional.of(Color.decode("#dd1c77"));
+ }
+
+ @Override
+ public Optional<Color> getTextColor() {
+ return Optional.of(Color.BLACK);
+ }
+
+ @Override
+ public Optional<AnalysisSampleUpdater> getUpdater(MetadataTemplateService metadataTemplateService,
+ SampleService sampleService, IridaWorkflowsService iridaWorkflowsService) throws IridaPluginException {
+ return Optional.of(new ExamplePluginUpdater(metadataTemplateService, sampleService, iridaWorkflowsService));
+ }
+}
+}
+```
+The purpose of each method is as follows:
+
+
+getAnalysisType(): This returns an AnalysisType object which stores the type of analysis as a String (matches the <analysisType>READ_INFO</analysisType> entry in the irida_workflow.xml file).
+
+
+getDefaultWorkflowUUID(): This returns the id of the workflow (matching the <id>79d90ca8-00ae-441b-b5c7-193c9e85a968</id> entry in the irida_workflow.xml file). Returning the appropriate value here is especially important if there are multiple versions of the same pipeline in this plugin (this will define the default or "latest" version).
+
+
+getBackgroundColor() and getTextColor(): The background and text color to display in the UI (defaults to grey for background and black for text). This is optional . See example below:
+
+
+
+
+getUpdater(): Gets an instance of a class used for post-processing on pipeline results (e.g., updating the IRIDA metadata). This is optional . Additional documentation about this class is described below.
+3. (Optional) Implement an Updater class
+An Updater class is used to perform post-processing on the resulting files, primarily intended to write back pipeline results into the IRIDA metadata system. Please see the ExamplePluginUpdater.java for an example implementation, or the built-in implementations in https://github.com/phac-nml/irida/tree/development/src/main/java/ca/corefacility/bioinformatics/irida/pipeline/results/impl . Implementing this class is optional for your pipeline.
+If you do implement this class, you will also want to make sure to update the messages_en.properties file with an entry like:
+properties
+workflow.label.share-analysis-samples.READ_INFO=Save sequence read information to Project Line List Metadata
+This contains the message to display asking the user if they wish to Save Results to Samples for their pipeline before launching the pipeline.
+
+4. Update the pom.xml file
+You will have to update the pom.xml file in order to set version information and other metadata about your pipeline.
+4.1. Update the Maven version/info
+You will want to update the Maven version/information section for this particular plugin. That is:
+xml
+<groupId>ca.corefacility.bioinformatics.irida.plugins</groupId>
+<artifactId>example-plugin</artifactId>
+<version>0.1.0-SNAPSHOT</version>
+Please see the Maven Documentation for more details.
+4.2. Update the properties section/plugin info
+The properties section contains additional information you will have to update. In particular:
+```xml
+example-plugin
+ca.corefacility.bioinformatics.irida.plugins.QIPhyloPlugin
+0.1.0
+Aaron Petkau
+1.0.0
+0.23.0-SNAPSHOT
+```
+The <plugin.*> entries contain information about your particular plugin as defined by PF4J .
+
+plugin.id: An identifier for your plugin.plugin.class: The fully-qualified name of the class implementing this plugin (in this case, the ExamplePlugin.java class).plugin.version: A version number for your plugin.plugin.provider: The provider of this plugin.plugin.dependencies: Other IRIDA plugins this plugin depends on.plugin.requires.runtime: The exact version of the IRIDA plugin API this plugin requires at runtime (stored in the IridaPlugin.java interface). You normally don't need to update this unless the version is also updated in IRIDA.
+The <irida.version.compiletime> contains the exact IRIDA version this plugin will need to be compiled against (compile-time version).
+5. Build and Test
+Once you've made all the updates, you can try building and testing your plugin. To build your plugin, you can run:
+bash
+mvn clean package
+You should find your packaged plugin JAR file in target/ (e.g., target/example-plugin-0.1.0-SNAPSHOT.jar).
+To test out this plugin, please copy to /etc/irida/plugins on a machine with IRIDA installed and restart IRIDA. Your plugin should show up in the Analyses > Pipelines page in IRIDA.
+
+You should also be able to see messages like below in the IRIDA log file when starting up:
+INFO org.pf4j.AbstractPluginManager:801 - Plugin 'example-plugin@0.1.0' resolved
+INFO org.pf4j.AbstractPluginManager:320 - Start plugin 'example-plugin@0.1.0'
+DEBUG ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig:45 - Loaded 1 valid pipeline plugins.
+6. Distribute
+Once you've successfully built your plugin, you can distribute the JAR file to other IRIDA users to install in their instances.
+
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..b4cce9a
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,85 @@
+
+
+ 4.0.0
+
+ ca.corefacility.bioinformatics.irida.plugins
+ qi-phylo
+ 0.1.0-SNAPSHOT
+
+
+
+
+ qi-phylo
+ ca.corefacility.bioinformatics.irida.plugins.QIPhyloPlugin
+ 0.2.0
+ Nabil-Fareed Alikhan
+ 1.0.0
+
+
+ 19.09-SNAPSHOT
+
+
+ 2.4.0
+
+
+ 1.8
+
+ UTF-8
+
+
+
+
+
+ ca.corefacility.bioinformatics
+ irida
+ ${irida.version.compiletime}
+ classes
+ provided
+
+
+
+ org.pf4j
+ pf4j
+ ${pf4j.version}
+ provided
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-compiler-plugin
+ 3.1
+
+ ${java.version}
+ ${java.version}
+ true
+
+
+
+
+ org.apache.maven.plugins
+ maven-jar-plugin
+ 3.1.1
+
+
+
+
+ ${plugin.class}
+ ${plugin.dependencies}
+ ${plugin.id}
+ ${plugin.provider}
+ ${plugin.version}
+ ${plugin.requires.runtime}
+
+
+
+
+
+
+
diff --git a/src/main/java/ca/corefacility/bioinformatics/irida/plugins/QIPhyloPlugin.java b/src/main/java/ca/corefacility/bioinformatics/irida/plugins/QIPhyloPlugin.java
new file mode 100644
index 0000000..b858a74
--- /dev/null
+++ b/src/main/java/ca/corefacility/bioinformatics/irida/plugins/QIPhyloPlugin.java
@@ -0,0 +1,110 @@
+package ca.corefacility.bioinformatics.irida.plugins;
+
+import java.awt.Color;
+import java.util.Optional;
+import java.util.UUID;
+
+import org.pf4j.Extension;
+import org.pf4j.Plugin;
+import org.pf4j.PluginWrapper;
+
+import ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType;
+import ca.corefacility.bioinformatics.irida.pipeline.results.updater.AnalysisSampleUpdater;
+import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
+import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
+import ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService;
+
+/**
+ * An example {@link IridaPlugin} implementation which will extract some
+ * information from the sequencing reads.
+ */
+public class QIPhyloPlugin extends Plugin {
+
+ /**
+ * The {@link AnalysisType} used by this plugin. This wraps around a string and
+ * is used to store the type of the analysis pipeline (which should be unique
+ * for each pipeline).
+ */
+ public static final AnalysisType QI_PHYLO = new AnalysisType("QI_PHYLO");
+
+ public QIPhyloPlugin(PluginWrapper wrapper) {
+ super(wrapper);
+ }
+
+ /**
+ * This class defines information about this particular plugin. On start-up,
+ * IRIDA will make use of the information provided by this class to integrate
+ * the plugin pipeline.
+ */
+ @Extension
+ public static class PluginInfo implements IridaPlugin {
+
+ /*******************************************************************************
+ * Required methods
+ *
+ * These methods are required to be overridden when implementing a pipeline as a
+ * plugin.
+ *******************************************************************************/
+
+ /**
+ * Gets the particular {@link AnalysisType} object for this workflow. This
+ * should correspond to the analysisType entry in the
+ * irida_workflow.xml file.
+ *
+ *
+ * {@code READ_INFO }
+ *
+ *
+ * @return The particular {@link AnalysisType} for this pipeline.
+ */
+ @Override
+ public AnalysisType getAnalysisType() {
+ return QI_PHYLO;
+ }
+
+ /**
+ * Gets the particular workflow id. This should correspond to the
+ * id entry in the irida_workflow.xml file.
+ *
+ *
+ * {@code 79d90ca8-00ae-441b-b5c7-193c9e85a968 }
+ *
+ *
+ * @return A {@link UUID} defining the id of this pipeline.
+ */
+ @Override
+ public UUID getDefaultWorkflowUUID() {
+ return UUID.fromString("83476350-794b-40b3-96b9-54c4ee94af59");
+ }
+
+ /*******************************************************************************
+ * Optional methods
+ *
+ * These methods are not required to be overridden but can be used to adjust the
+ * appearance/behavior of the pipeline.
+ *******************************************************************************/
+
+ /**
+ * Defines the background color in the IRIDA UI corresponding to this pipeline.
+ *
+ * @return An {@link Optional} color for the background of the IRIDA UI for this
+ * pipeline.
+ */
+ @Override
+ public Optional getBackgroundColor() {
+ return Optional.of(Color.decode("#b7a7b2"));
+ }
+
+ /**
+ * Defines the text color in the IRIDA UI corresponding to this pipeline.
+ *
+ * @return An {@link Optional} color for the text of the IRIDA UI for this
+ * pipeline.
+ */
+ @Override
+ public Optional getTextColor() {
+ return Optional.of(Color.BLACK);
+ }
+
+ }
+}
diff --git a/src/main/resources/workflows/0.1/irida_workflow.xml b/src/main/resources/workflows/0.1/irida_workflow.xml
new file mode 100644
index 0000000..92067f8
--- /dev/null
+++ b/src/main/resources/workflows/0.1/irida_workflow.xml
@@ -0,0 +1,263 @@
+
+ 8ede0691-cc85-4ac2-a423-f33a91dea7e4
+ QIPhylo
+ 0.1
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 37e42abdce08
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.1/irida_workflow_structure.ga b/src/main/resources/workflows/0.1/irida_workflow_structure.ga
new file mode 100644
index 0000000..9d34c57
--- /dev/null
+++ b/src/main/resources/workflows/0.1/irida_workflow_structure.ga
@@ -0,0 +1,460 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "dff0da45-bc59-423b-b7d9-6e58da529feb"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "252941f3-c784-437a-8642-58f5aa1deed6"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool snippy",
+ "name": "ref"
+ },
+ {
+ "description": "runtime parameter for tool snippy",
+ "name": "fastq_input"
+ }
+ ],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snpgff",
+ "type": "gff3"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "snpsum",
+ "type": "tabular"
+ },
+ {
+ "name": "snplog",
+ "type": "txt"
+ },
+ {
+ "name": "snpalign",
+ "type": "fasta"
+ },
+ {
+ "name": "snpconsensus",
+ "type": "fasta"
+ },
+ {
+ "name": "snpsdepth",
+ "type": "tabular"
+ },
+ {
+ "name": "snpsbam",
+ "type": "bam"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnpalign": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpalign"
+ },
+ "HideDatasetActionsnpconsensus": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpconsensus"
+ },
+ "HideDatasetActionsnpgff": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpgff"
+ },
+ "HideDatasetActionsnplog": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snplog"
+ },
+ "HideDatasetActionsnpsbam": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpsbam"
+ },
+ "HideDatasetActionsnpsdepth": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpsdepth"
+ },
+ "HideDatasetActionsnpsum": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpsum"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool snippy-core",
+ "name": "indirs"
+ }
+ ],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "full_alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "HideDatasetActionfull_alignment_fasta": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "full_alignment_fasta"
+ },
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1308.5,
+ "top": 240
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "contree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "mldist.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "splits.nex"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "tree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "tool_shed_repository": {
+ "changeset_revision": "37e42abdce08",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 1, \\\"m\\\": \\\"\\\", \\\"opt_custommodel\\\": \\\"false\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "0bebf65c-40a4-4a8e-a7b7-77e312afc4e0",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "3bd6175b-8275-4264-bfcd-65f661accef0"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "5a0e4639-d068-410e-b480-5bbd8ca23eb2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "783b4dd0-ae11-4a8b-b10e-e5859b8243b6"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "1b2c669a-d1d6-47e6-96ed-0dcf77666d39"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "6301c062-9414-44d9-9905-100f4eed14ae"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "7f9ef5c3-47b9-44ed-816b-41bc8e36400d"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "79de3809-f91a-41ad-941b-fdac758a4ccc",
+ "version": 3
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.1/messages_en.properties b/src/main/resources/workflows/0.1/messages_en.properties
new file mode 100644
index 0000000..8e2ef1b
--- /dev/null
+++ b/src/main/resources/workflows/0.1/messages_en.properties
@@ -0,0 +1,88 @@
+#Pipeline Info Properties
+#Thu Jul 04 14:23:10 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Thu Jul 04 14:23:10 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Thu Jul 04 14:23:10 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Thu Jul 04 14:23:10 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.10/irida_workflow.xml b/src/main/resources/workflows/0.10/irida_workflow.xml
new file mode 100644
index 0000000..a0a7443
--- /dev/null
+++ b/src/main/resources/workflows/0.10/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ 54bb0ebf-ed18-44f6-89b1-1969f1fc4187
+ QIPhylo
+ 0.10
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.10/irida_workflow_structure.ga b/src/main/resources/workflows/0.10/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.10/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.10/messages_en.properties b/src/main/resources/workflows/0.10/messages_en.properties
new file mode 100644
index 0000000..ba2cce0
--- /dev/null
+++ b/src/main/resources/workflows/0.10/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Mon Sep 09 11:19:52 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=Fast phylogeny pipeline (Snippy, IQTree) v0.10
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Mon Sep 09 11:19:52 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Mon Sep 09 11:19:52 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Mon Sep 09 11:19:52 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.11/irida_workflow.xml b/src/main/resources/workflows/0.11/irida_workflow.xml
new file mode 100644
index 0000000..a047923
--- /dev/null
+++ b/src/main/resources/workflows/0.11/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ 83476350-794b-40b3-96b9-54c4ee94af59
+ QIPhylo
+ 0.11
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.11/irida_workflow_structure.ga b/src/main/resources/workflows/0.11/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.11/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.11/messages_en.properties b/src/main/resources/workflows/0.11/messages_en.properties
new file mode 100644
index 0000000..0a7d10a
--- /dev/null
+++ b/src/main/resources/workflows/0.11/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Mon Sep 09 11:22:20 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=Fast phylogeny pipeline (Snippy, IQTree) v0.11
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Mon Sep 09 11:22:20 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Mon Sep 09 11:22:20 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Mon Sep 09 11:22:20 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.12/irida_workflow.xml b/src/main/resources/workflows/0.12/irida_workflow.xml
new file mode 100644
index 0000000..90cf8b9
--- /dev/null
+++ b/src/main/resources/workflows/0.12/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ f94e7dc2-9ffd-418c-a349-c529aab5739f
+ QIPhylo
+ 0.12
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.12/irida_workflow_structure.ga b/src/main/resources/workflows/0.12/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.12/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.12/messages_en.properties b/src/main/resources/workflows/0.12/messages_en.properties
new file mode 100644
index 0000000..8a85f3d
--- /dev/null
+++ b/src/main/resources/workflows/0.12/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Mon Sep 09 14:08:23 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Mon Sep 09 14:08:23 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Mon Sep 09 14:08:23 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Mon Sep 09 14:08:23 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.13/irida_workflow.xml b/src/main/resources/workflows/0.13/irida_workflow.xml
new file mode 100644
index 0000000..7b4bca4
--- /dev/null
+++ b/src/main/resources/workflows/0.13/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ 6ff310d4-2368-4e5b-b6d7-9c0d75874ce3
+ QIPhylo
+ 0.13
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.13/irida_workflow_structure.ga b/src/main/resources/workflows/0.13/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.13/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.13/messages_en.properties b/src/main/resources/workflows/0.13/messages_en.properties
new file mode 100644
index 0000000..a74d141
--- /dev/null
+++ b/src/main/resources/workflows/0.13/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Mon Sep 09 14:13:59 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Mon Sep 09 14:13:59 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Mon Sep 09 14:13:59 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Mon Sep 09 14:13:59 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.14/irida_workflow.xml b/src/main/resources/workflows/0.14/irida_workflow.xml
new file mode 100644
index 0000000..586ad4d
--- /dev/null
+++ b/src/main/resources/workflows/0.14/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ c802eeb9-ba1f-441c-b679-2eb5d52646d0
+ QIPhylo
+ 0.14
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.14/irida_workflow_structure.ga b/src/main/resources/workflows/0.14/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.14/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.14/messages_en.properties b/src/main/resources/workflows/0.14/messages_en.properties
new file mode 100644
index 0000000..f9af264
--- /dev/null
+++ b/src/main/resources/workflows/0.14/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Mon Sep 09 14:37:36 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Mon Sep 09 14:37:36 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Mon Sep 09 14:37:36 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Mon Sep 09 14:37:36 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.15/irida_workflow.xml b/src/main/resources/workflows/0.15/irida_workflow.xml
new file mode 100644
index 0000000..a1cffab
--- /dev/null
+++ b/src/main/resources/workflows/0.15/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ 34b8964a-6750-49a3-b1a3-562ade7bcbab
+ QIPhylo
+ 0.15
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.15/irida_workflow_structure.ga b/src/main/resources/workflows/0.15/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.15/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.15/messages_en.properties b/src/main/resources/workflows/0.15/messages_en.properties
new file mode 100644
index 0000000..1835162
--- /dev/null
+++ b/src/main/resources/workflows/0.15/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Mon Sep 09 14:54:56 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Mon Sep 09 14:54:56 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Mon Sep 09 14:54:56 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Mon Sep 09 14:54:56 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.16/irida_workflow.xml b/src/main/resources/workflows/0.16/irida_workflow.xml
new file mode 100644
index 0000000..2f226fe
--- /dev/null
+++ b/src/main/resources/workflows/0.16/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ 8e01d923-2c4c-4529-923e-aaec4b604d1e
+ QIPhylo
+ 0.16
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.16/irida_workflow_structure.ga b/src/main/resources/workflows/0.16/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.16/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.16/messages_en.properties b/src/main/resources/workflows/0.16/messages_en.properties
new file mode 100644
index 0000000..9599a54
--- /dev/null
+++ b/src/main/resources/workflows/0.16/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Mon Sep 09 16:02:02 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Mon Sep 09 16:02:02 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Mon Sep 09 16:02:02 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Mon Sep 09 16:02:02 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.17/irida_workflow.xml b/src/main/resources/workflows/0.17/irida_workflow.xml
new file mode 100644
index 0000000..4107ae9
--- /dev/null
+++ b/src/main/resources/workflows/0.17/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ e40c462d-6d11-4aad-a87a-f1e5756e0b5e
+ QIPhylo
+ 0.17
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.17/irida_workflow_structure.ga b/src/main/resources/workflows/0.17/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.17/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.17/messages_en.properties b/src/main/resources/workflows/0.17/messages_en.properties
new file mode 100644
index 0000000..c077a00
--- /dev/null
+++ b/src/main/resources/workflows/0.17/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Fri Sep 13 13:37:40 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Fri Sep 13 13:37:40 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Fri Sep 13 13:37:40 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Fri Sep 13 13:37:40 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.18/irida_workflow.xml b/src/main/resources/workflows/0.18/irida_workflow.xml
new file mode 100644
index 0000000..bc0143c
--- /dev/null
+++ b/src/main/resources/workflows/0.18/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ 5a6c986b-bea2-477d-9d64-cba56eca2ba1
+ QIPhylo
+ 0.18
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.18/irida_workflow_structure.ga b/src/main/resources/workflows/0.18/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.18/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.18/messages_en.properties b/src/main/resources/workflows/0.18/messages_en.properties
new file mode 100644
index 0000000..6f001da
--- /dev/null
+++ b/src/main/resources/workflows/0.18/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Fri Sep 13 14:13:59 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Fri Sep 13 14:13:59 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Fri Sep 13 14:13:59 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Fri Sep 13 14:13:59 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.19/irida_workflow.xml b/src/main/resources/workflows/0.19/irida_workflow.xml
new file mode 100644
index 0000000..95c5124
--- /dev/null
+++ b/src/main/resources/workflows/0.19/irida_workflow.xml
@@ -0,0 +1,266 @@
+
+ 9769036f-19a3-4ad5-9b13-0d3311dc51ad
+ QIPhylo
+ 0.19
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 87daf702e477
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.19/irida_workflow_structure.ga b/src/main/resources/workflows/0.19/irida_workflow_structure.ga
new file mode 100644
index 0000000..816ea6c
--- /dev/null
+++ b/src/main/resources/workflows/0.19/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "bb6527ee-c776-450b-b26d-2f921145cc28"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "99ee65bf-a25a-4de9-91ba-466588140ab4"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1409,
+ "top": 145
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "consensus.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "iqtree.mldist"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "bootstrap.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "mltree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12",
+ "tool_shed_repository": {
+ "changeset_revision": "87daf702e477",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"fast\\\": \\\"true\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.12",
+ "type": "tool",
+ "uuid": "220797f8-a79b-4c2f-8279-4a51b3f0645a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "ce01f9aa-f72e-4646-b371-c872e9615f16"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "81b003f2-c8b7-4a89-80cd-547b28fcc3c2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "f5bbacb0-d0f4-4992-bd34-b8a6dc4935ae"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "2dd7934e-2f1b-4eed-a390-7bc5d3fd82a5"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "3376b142-b48a-4f76-ad41-19c54980ec28"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "dbba944f-75a4-4685-ad8f-1ada2306f53f"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "a62d7618-f6b6-4a95-b264-fb17e2ca9b43",
+ "version": 7
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.19/messages_en.properties b/src/main/resources/workflows/0.19/messages_en.properties
new file mode 100644
index 0000000..5ff43d4
--- /dev/null
+++ b/src/main/resources/workflows/0.19/messages_en.properties
@@ -0,0 +1,89 @@
+#Pipeline Info Properties
+#Fri Sep 13 15:54:00 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Fri Sep 13 15:54:00 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Fri Sep 13 15:54:00 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Fri Sep 13 15:54:00 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.fast=iqtree-4-tree_parameters.tree_search.fast
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.2/irida_workflow.xml b/src/main/resources/workflows/0.2/irida_workflow.xml
new file mode 100644
index 0000000..e4429d0
--- /dev/null
+++ b/src/main/resources/workflows/0.2/irida_workflow.xml
@@ -0,0 +1,263 @@
+
+ 79400b89-b186-4bf1-aaab-c8746ab8ed22
+ QIPhylo
+ 0.2
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 37e42abdce08
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.2/irida_workflow_structure.ga b/src/main/resources/workflows/0.2/irida_workflow_structure.ga
new file mode 100644
index 0000000..56edc76
--- /dev/null
+++ b/src/main/resources/workflows/0.2/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "32912714-9403-4be8-8fdb-5da63c3e08f7"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "ce729d06-a453-4570-81f8-71ce8e08ae58"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1308.5,
+ "top": 240
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "contree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "mldist.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "splits.nex"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "tree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "tool_shed_repository": {
+ "changeset_revision": "37e42abdce08",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.10",
+ "type": "tool",
+ "uuid": "0bebf65c-40a4-4a8e-a7b7-77e312afc4e0",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "3bd6175b-8275-4264-bfcd-65f661accef0"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "5a0e4639-d068-410e-b480-5bbd8ca23eb2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "783b4dd0-ae11-4a8b-b10e-e5859b8243b6"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "1b2c669a-d1d6-47e6-96ed-0dcf77666d39"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "6301c062-9414-44d9-9905-100f4eed14ae"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "7f9ef5c3-47b9-44ed-816b-41bc8e36400d"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "2212b1f0-3937-442e-b4a8-b08bd6e592c5",
+ "version": 4
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.2/messages_en.properties b/src/main/resources/workflows/0.2/messages_en.properties
new file mode 100644
index 0000000..55784f1
--- /dev/null
+++ b/src/main/resources/workflows/0.2/messages_en.properties
@@ -0,0 +1,88 @@
+#Pipeline Info Properties
+#Thu Sep 05 15:03:35 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Thu Sep 05 15:03:35 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Thu Sep 05 15:03:35 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Thu Sep 05 15:03:35 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.3/irida_workflow.xml b/src/main/resources/workflows/0.3/irida_workflow.xml
new file mode 100644
index 0000000..ea57354
--- /dev/null
+++ b/src/main/resources/workflows/0.3/irida_workflow.xml
@@ -0,0 +1,263 @@
+
+ dae2c6a6-b2bb-47a7-802a-57f2394e2ea4
+ QIPhylo
+ 0.3
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 37e42abdce08
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.3/irida_workflow_structure.ga b/src/main/resources/workflows/0.3/irida_workflow_structure.ga
new file mode 100644
index 0000000..56edc76
--- /dev/null
+++ b/src/main/resources/workflows/0.3/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "32912714-9403-4be8-8fdb-5da63c3e08f7"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "ce729d06-a453-4570-81f8-71ce8e08ae58"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1308.5,
+ "top": 240
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "contree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "mldist.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "splits.nex"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "tree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "tool_shed_repository": {
+ "changeset_revision": "37e42abdce08",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.10",
+ "type": "tool",
+ "uuid": "0bebf65c-40a4-4a8e-a7b7-77e312afc4e0",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "3bd6175b-8275-4264-bfcd-65f661accef0"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "5a0e4639-d068-410e-b480-5bbd8ca23eb2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "783b4dd0-ae11-4a8b-b10e-e5859b8243b6"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "1b2c669a-d1d6-47e6-96ed-0dcf77666d39"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "6301c062-9414-44d9-9905-100f4eed14ae"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "7f9ef5c3-47b9-44ed-816b-41bc8e36400d"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "2212b1f0-3937-442e-b4a8-b08bd6e592c5",
+ "version": 4
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.3/messages_en.properties b/src/main/resources/workflows/0.3/messages_en.properties
new file mode 100644
index 0000000..1faf573
--- /dev/null
+++ b/src/main/resources/workflows/0.3/messages_en.properties
@@ -0,0 +1,88 @@
+#Pipeline Info Properties
+#Thu Sep 05 15:06:43 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Thu Sep 05 15:06:43 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Thu Sep 05 15:06:43 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Thu Sep 05 15:06:43 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.4/irida_workflow.xml b/src/main/resources/workflows/0.4/irida_workflow.xml
new file mode 100644
index 0000000..699e5ae
--- /dev/null
+++ b/src/main/resources/workflows/0.4/irida_workflow.xml
@@ -0,0 +1,263 @@
+
+ 553042e8-f42d-4a13-85cf-939df7623e6b
+ QIPhylo
+ 0.4
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 37e42abdce08
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.4/irida_workflow_structure.ga b/src/main/resources/workflows/0.4/irida_workflow_structure.ga
new file mode 100644
index 0000000..56edc76
--- /dev/null
+++ b/src/main/resources/workflows/0.4/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "32912714-9403-4be8-8fdb-5da63c3e08f7"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "ce729d06-a453-4570-81f8-71ce8e08ae58"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1308.5,
+ "top": 240
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "contree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "mldist.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "splits.nex"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "tree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "tool_shed_repository": {
+ "changeset_revision": "37e42abdce08",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.10",
+ "type": "tool",
+ "uuid": "0bebf65c-40a4-4a8e-a7b7-77e312afc4e0",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "3bd6175b-8275-4264-bfcd-65f661accef0"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "5a0e4639-d068-410e-b480-5bbd8ca23eb2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "783b4dd0-ae11-4a8b-b10e-e5859b8243b6"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "1b2c669a-d1d6-47e6-96ed-0dcf77666d39"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "6301c062-9414-44d9-9905-100f4eed14ae"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "7f9ef5c3-47b9-44ed-816b-41bc8e36400d"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "2212b1f0-3937-442e-b4a8-b08bd6e592c5",
+ "version": 4
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.4/messages_en.properties b/src/main/resources/workflows/0.4/messages_en.properties
new file mode 100644
index 0000000..2e0fb60
--- /dev/null
+++ b/src/main/resources/workflows/0.4/messages_en.properties
@@ -0,0 +1,88 @@
+#Pipeline Info Properties
+#Thu Sep 05 15:11:25 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=Fast phylogeny pipeline (Snippy, IQTree) v0.4
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Thu Sep 05 15:11:25 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Thu Sep 05 15:11:25 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Thu Sep 05 15:11:25 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.5/irida_workflow.xml b/src/main/resources/workflows/0.5/irida_workflow.xml
new file mode 100644
index 0000000..0f43603
--- /dev/null
+++ b/src/main/resources/workflows/0.5/irida_workflow.xml
@@ -0,0 +1,263 @@
+
+ fb0aada1-9ad5-4a07-abf1-621ed71ab19c
+ QIPhylo
+ 0.5
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 37e42abdce08
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.5/irida_workflow_structure.ga b/src/main/resources/workflows/0.5/irida_workflow_structure.ga
new file mode 100644
index 0000000..56edc76
--- /dev/null
+++ b/src/main/resources/workflows/0.5/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "32912714-9403-4be8-8fdb-5da63c3e08f7"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "ce729d06-a453-4570-81f8-71ce8e08ae58"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1308.5,
+ "top": 240
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "contree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "mldist.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "splits.nex"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "tree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "tool_shed_repository": {
+ "changeset_revision": "37e42abdce08",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.10",
+ "type": "tool",
+ "uuid": "0bebf65c-40a4-4a8e-a7b7-77e312afc4e0",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "3bd6175b-8275-4264-bfcd-65f661accef0"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "5a0e4639-d068-410e-b480-5bbd8ca23eb2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "783b4dd0-ae11-4a8b-b10e-e5859b8243b6"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "1b2c669a-d1d6-47e6-96ed-0dcf77666d39"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "6301c062-9414-44d9-9905-100f4eed14ae"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "7f9ef5c3-47b9-44ed-816b-41bc8e36400d"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "2212b1f0-3937-442e-b4a8-b08bd6e592c5",
+ "version": 4
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.5/messages_en.properties b/src/main/resources/workflows/0.5/messages_en.properties
new file mode 100644
index 0000000..6f68c80
--- /dev/null
+++ b/src/main/resources/workflows/0.5/messages_en.properties
@@ -0,0 +1,88 @@
+#Pipeline Info Properties
+#Thu Sep 05 15:14:40 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=Fast phylogeny pipeline (Snippy, IQTree) v0.5
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Thu Sep 05 15:14:40 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Thu Sep 05 15:14:40 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Thu Sep 05 15:14:40 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.6/irida_workflow.xml b/src/main/resources/workflows/0.6/irida_workflow.xml
new file mode 100644
index 0000000..f1b7f70
--- /dev/null
+++ b/src/main/resources/workflows/0.6/irida_workflow.xml
@@ -0,0 +1,263 @@
+
+ 91e87ef9-b8cd-4a4b-b635-c3979eba754b
+ QIPhylo
+ 0.6
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 37e42abdce08
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.6/irida_workflow_structure.ga b/src/main/resources/workflows/0.6/irida_workflow_structure.ga
new file mode 100644
index 0000000..56edc76
--- /dev/null
+++ b/src/main/resources/workflows/0.6/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "32912714-9403-4be8-8fdb-5da63c3e08f7"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "ce729d06-a453-4570-81f8-71ce8e08ae58"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1308.5,
+ "top": 240
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "contree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "mldist.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "splits.nex"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "tree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "tool_shed_repository": {
+ "changeset_revision": "37e42abdce08",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.10",
+ "type": "tool",
+ "uuid": "0bebf65c-40a4-4a8e-a7b7-77e312afc4e0",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "3bd6175b-8275-4264-bfcd-65f661accef0"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "5a0e4639-d068-410e-b480-5bbd8ca23eb2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "783b4dd0-ae11-4a8b-b10e-e5859b8243b6"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "1b2c669a-d1d6-47e6-96ed-0dcf77666d39"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "6301c062-9414-44d9-9905-100f4eed14ae"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "7f9ef5c3-47b9-44ed-816b-41bc8e36400d"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "2212b1f0-3937-442e-b4a8-b08bd6e592c5",
+ "version": 4
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.6/messages_en.properties b/src/main/resources/workflows/0.6/messages_en.properties
new file mode 100644
index 0000000..f9a8fdd
--- /dev/null
+++ b/src/main/resources/workflows/0.6/messages_en.properties
@@ -0,0 +1,88 @@
+#Pipeline Info Properties
+#Thu Sep 05 15:24:46 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=Fast phylogeny pipeline (Snippy, IQTree) v0.6
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Thu Sep 05 15:24:46 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Thu Sep 05 15:24:46 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Thu Sep 05 15:24:46 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.7/irida_workflow.xml b/src/main/resources/workflows/0.7/irida_workflow.xml
new file mode 100644
index 0000000..a833f2c
--- /dev/null
+++ b/src/main/resources/workflows/0.7/irida_workflow.xml
@@ -0,0 +1,263 @@
+
+ a32947c7-3697-4b63-a6ea-6da8cef5bf13
+ QIPhylo
+ 0.7
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 37e42abdce08
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.7/irida_workflow_structure.ga b/src/main/resources/workflows/0.7/irida_workflow_structure.ga
new file mode 100644
index 0000000..7e371b0
--- /dev/null
+++ b/src/main/resources/workflows/0.7/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "dd26e811-1bfa-471e-ac38-34356f683c10"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "93a4d067-661d-49c5-8b6e-7109566a8ddc"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1308.5,
+ "top": 240
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "contree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "mldist.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "splits.nex"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "tree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "tool_shed_repository": {
+ "changeset_revision": "37e42abdce08",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"10\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"0\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.10",
+ "type": "tool",
+ "uuid": "0bebf65c-40a4-4a8e-a7b7-77e312afc4e0",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "3bd6175b-8275-4264-bfcd-65f661accef0"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "5a0e4639-d068-410e-b480-5bbd8ca23eb2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "783b4dd0-ae11-4a8b-b10e-e5859b8243b6"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "1b2c669a-d1d6-47e6-96ed-0dcf77666d39"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "6301c062-9414-44d9-9905-100f4eed14ae"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "7f9ef5c3-47b9-44ed-816b-41bc8e36400d"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "0e2458dc-256e-486e-891d-972271db1a33",
+ "version": 5
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.7/messages_en.properties b/src/main/resources/workflows/0.7/messages_en.properties
new file mode 100644
index 0000000..d0d627b
--- /dev/null
+++ b/src/main/resources/workflows/0.7/messages_en.properties
@@ -0,0 +1,88 @@
+#Pipeline Info Properties
+#Thu Sep 05 15:53:18 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=Fast phylogeny pipeline (Snippy, IQTree) v0.7
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Thu Sep 05 15:53:18 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Thu Sep 05 15:53:18 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Thu Sep 05 15:53:18 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.8/irida_workflow.xml b/src/main/resources/workflows/0.8/irida_workflow.xml
new file mode 100644
index 0000000..98a7a56
--- /dev/null
+++ b/src/main/resources/workflows/0.8/irida_workflow.xml
@@ -0,0 +1,263 @@
+
+ b5c89708-9e5c-4337-8b4a-538e5d8a85b7
+ QIPhylo
+ 0.8
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 37e42abdce08
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.8/irida_workflow_structure.ga b/src/main/resources/workflows/0.8/irida_workflow_structure.ga
new file mode 100644
index 0000000..7e371b0
--- /dev/null
+++ b/src/main/resources/workflows/0.8/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "dd26e811-1bfa-471e-ac38-34356f683c10"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "93a4d067-661d-49c5-8b6e-7109566a8ddc"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1308.5,
+ "top": 240
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "contree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "mldist.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "splits.nex"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "tree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "tool_shed_repository": {
+ "changeset_revision": "37e42abdce08",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"10\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"0\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.10",
+ "type": "tool",
+ "uuid": "0bebf65c-40a4-4a8e-a7b7-77e312afc4e0",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "3bd6175b-8275-4264-bfcd-65f661accef0"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "5a0e4639-d068-410e-b480-5bbd8ca23eb2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "783b4dd0-ae11-4a8b-b10e-e5859b8243b6"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "1b2c669a-d1d6-47e6-96ed-0dcf77666d39"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "6301c062-9414-44d9-9905-100f4eed14ae"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "7f9ef5c3-47b9-44ed-816b-41bc8e36400d"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "0e2458dc-256e-486e-891d-972271db1a33",
+ "version": 5
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.8/messages_en.properties b/src/main/resources/workflows/0.8/messages_en.properties
new file mode 100644
index 0000000..66fca6b
--- /dev/null
+++ b/src/main/resources/workflows/0.8/messages_en.properties
@@ -0,0 +1,88 @@
+#Pipeline Info Properties
+#Mon Sep 09 11:01:36 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=Fast phylogeny pipeline (Snippy, IQTree) v0.8
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Mon Sep 09 11:01:36 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Mon Sep 09 11:01:36 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Mon Sep 09 11:01:36 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
diff --git a/src/main/resources/workflows/0.9/irida_workflow.xml b/src/main/resources/workflows/0.9/irida_workflow.xml
new file mode 100644
index 0000000..7b4441e
--- /dev/null
+++ b/src/main/resources/workflows/0.9/irida_workflow.xml
@@ -0,0 +1,263 @@
+
+ 0bf9356d-6545-4773-9789-d996b48d138b
+ QIPhylo
+ 0.9
+ QI_PHYLO
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 82f2b6f20fa2
+
+
+ iqtree
+ leomrtns
+ https://testtoolshed.g2.bx.psu.edu
+ 37e42abdce08
+
+
+
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.9/irida_workflow_structure.ga b/src/main/resources/workflows/0.9/irida_workflow_structure.ga
new file mode 100644
index 0000000..7e371b0
--- /dev/null
+++ b/src/main/resources/workflows/0.9/irida_workflow_structure.ga
@@ -0,0 +1,374 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "qi-phylo",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "reference"
+ }
+ ],
+ "label": "reference",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"name\": \"reference\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "fe8d4677-4c85-42e9-af65-a0da55443aef",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "dd26e811-1bfa-471e-ac38-34356f683c10"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "sequence_reads_paired"
+ }
+ ],
+ "label": "sequence_reads_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 243,
+ "top": 570
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "36e8971c-79b9-48cd-94d2-11ceb3e707f3",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "93a4d067-661d-49c5-8b6e-7109566a8ddc"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "fastq_input|fastq_input": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "ref": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy",
+ "outputs": [
+ {
+ "name": "snpvcf",
+ "type": "vcf"
+ },
+ {
+ "name": "snptab",
+ "type": "tabular"
+ },
+ {
+ "name": "outdir",
+ "type": "zip"
+ }
+ ],
+ "position": {
+ "left": 523.5,
+ "top": 434
+ },
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "outdir"
+ },
+ "HideDatasetActionsnptab": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snptab"
+ },
+ "HideDatasetActionsnpvcf": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "snpvcf"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"ref\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "tool_version": "3.2+galaxy1",
+ "type": "tool",
+ "uuid": "8be43971-d993-4d33-8912-91355f714e50",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "indirs": {
+ "id": 2,
+ "output_name": "outdir"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "snippy-core",
+ "outputs": [
+ {
+ "name": "alignment_fasta",
+ "type": "fasta"
+ },
+ {
+ "name": "alignment_table",
+ "type": "tabular"
+ },
+ {
+ "name": "alignment_summary",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 919.5,
+ "top": 422
+ },
+ "post_job_actions": {
+ "RenameDatasetActionalignment_fasta": {
+ "action_arguments": {
+ "newname": "core.fasta"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_fasta"
+ },
+ "RenameDatasetActionalignment_summary": {
+ "action_arguments": {
+ "newname": "core_sum.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_summary"
+ },
+ "RenameDatasetActionalignment_table": {
+ "action_arguments": {
+ "newname": "core.tsv"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "alignment_table"
+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2",
+ "tool_shed_repository": {
+ "changeset_revision": "82f2b6f20fa2",
+ "name": "snippy",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"outputs\": \"[\\\"outaln\\\", \\\"outtab\\\", \\\"outtxt\\\"]\", \"is_reference\": \"\\\"false\\\"\", \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+ "tool_version": "3.2",
+ "type": "tool",
+ "uuid": "3aa7ef26-9836-4373-be21-f4deb12edd20",
+ "workflow_outputs": [
+ {
+ "label": "align_table",
+ "output_name": "alignment_table",
+ "uuid": "07671ed7-7513-4051-b5f2-83d1b54e6e5a"
+ },
+ {
+ "label": "align_fas",
+ "output_name": "alignment_fasta",
+ "uuid": "c8e420ae-4275-4aae-aa5f-97f9e450f449"
+ },
+ {
+ "label": "align_sum",
+ "output_name": "alignment_summary",
+ "uuid": "d32b9891-38fa-49b1-b8ad-6cb7b86d09ed"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "general_options|s": {
+ "id": 3,
+ "output_name": "alignment_fasta"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "general_options"
+ },
+ {
+ "description": "runtime parameter for tool IQ-TREE",
+ "name": "likelihood_mapping"
+ }
+ ],
+ "label": null,
+ "name": "IQ-TREE",
+ "outputs": [
+ {
+ "name": "bionj",
+ "type": "nhx"
+ },
+ {
+ "name": "treefile",
+ "type": "nhx"
+ },
+ {
+ "name": "contree",
+ "type": "nhx"
+ },
+ {
+ "name": "mldist",
+ "type": "mldist"
+ },
+ {
+ "name": "splits.nex",
+ "type": "nex"
+ },
+ {
+ "name": "iqtree",
+ "type": "iqtree"
+ }
+ ],
+ "position": {
+ "left": 1308.5,
+ "top": 240
+ },
+ "post_job_actions": {
+ "RenameDatasetActionbionj": {
+ "action_arguments": {
+ "newname": "bionj.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "bionj"
+ },
+ "RenameDatasetActioncontree": {
+ "action_arguments": {
+ "newname": "contree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "contree"
+ },
+ "RenameDatasetActioniqtree": {
+ "action_arguments": {
+ "newname": "iqtree.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "iqtree"
+ },
+ "RenameDatasetActionmldist": {
+ "action_arguments": {
+ "newname": "mldist.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "mldist"
+ },
+ "RenameDatasetActionsplits.nex": {
+ "action_arguments": {
+ "newname": "splits.nex"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "splits.nex"
+ },
+ "RenameDatasetActiontreefile": {
+ "action_arguments": {
+ "newname": "tree.newick"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "treefile"
+ }
+ },
+ "tool_id": "testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.10",
+ "tool_shed_repository": {
+ "changeset_revision": "37e42abdce08",
+ "name": "iqtree",
+ "owner": "leomrtns",
+ "tool_shed": "testtoolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"HKY\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"10\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"0\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "tool_version": "1.6.10",
+ "type": "tool",
+ "uuid": "0bebf65c-40a4-4a8e-a7b7-77e312afc4e0",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "iqtree",
+ "uuid": "3bd6175b-8275-4264-bfcd-65f661accef0"
+ },
+ {
+ "label": null,
+ "output_name": "splits.nex",
+ "uuid": "5a0e4639-d068-410e-b480-5bbd8ca23eb2"
+ },
+ {
+ "label": null,
+ "output_name": "mldist",
+ "uuid": "783b4dd0-ae11-4a8b-b10e-e5859b8243b6"
+ },
+ {
+ "label": null,
+ "output_name": "treefile",
+ "uuid": "1b2c669a-d1d6-47e6-96ed-0dcf77666d39"
+ },
+ {
+ "label": null,
+ "output_name": "bionj",
+ "uuid": "6301c062-9414-44d9-9905-100f4eed14ae"
+ },
+ {
+ "label": null,
+ "output_name": "contree",
+ "uuid": "7f9ef5c3-47b9-44ed-816b-41bc8e36400d"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "0e2458dc-256e-486e-891d-972271db1a33",
+ "version": 5
+}
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.9/messages_en.properties b/src/main/resources/workflows/0.9/messages_en.properties
new file mode 100644
index 0000000..0434526
--- /dev/null
+++ b/src/main/resources/workflows/0.9/messages_en.properties
@@ -0,0 +1,88 @@
+#Pipeline Info Properties
+#Mon Sep 09 11:02:16 BST 2019
+pipeline.parameters.modal-title.qiphylo=QIPhylo Pipeline Parameters
+pipeline.title.QIPhylo=Pipelines - QIPhylo
+pipeline.h1.QIPhylo=QIPhylo Pipeline
+workflow.QI_PHYLO.description=Fast phylogeny pipeline (Snippy, IQTree) v0.9
+workflow.QI_PHYLO.title=QIPhylo Pipeline
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Mon Sep 09 11:02:16 BST 2019
+pipeline.parameters.qiphylo.snippy-2-adv.mincov=snippy-2-adv.mincov
+pipeline.parameters.qiphylo.snippy-2-fastq_input.fastq_input_selector=snippy-2-fastq_input.fastq_input_selector
+pipeline.parameters.qiphylo.snippy-2-adv.mapqual=snippy-2-adv.mapqual
+pipeline.parameters.qiphylo.snippy-2-adv.minfrac=snippy-2-adv.minfrac
+pipeline.parameters.qiphylo.snippy-2-adv.bwaopt=snippy-2-adv.bwaopt
+pipeline.parameters.qiphylo.snippy-2-adv.rgid=snippy-2-adv.rgid
+#Tool Parameters - Tool: snippy - Workflow Step #: 3
+#Mon Sep 09 11:02:16 BST 2019
+pipeline.parameters.qiphylo.snippy-3-is_reference=snippy-3-is_reference
+#Tool Parameters - Tool: iqtree - Workflow Step #: 4
+#Mon Sep 09 11:02:16 BST 2019
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mset=iqtree-4-modelling_parameters.automatic_model.mset
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mtree=iqtree-4-modelling_parameters.automatic_model.mtree
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.djc=iqtree-4-tree_parameters.tree_search.djc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_all=iqtree-4-tree_parameters.computing_robinson_foulds.rf_all
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.rcluster=iqtree-4-modelling_parameters.automatic_model.rcluster
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.r=iqtree-4-tree_parameters.generating_random.r
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rbal=iqtree-4-tree_parameters.generating_random.rbal
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mfreq=iqtree-4-modelling_parameters.automatic_model.mfreq
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcsg=iqtree-4-tree_parameters.generating_random.rcsg
+pipeline.parameters.qiphylo.iqtree-4-general_options.seed=iqtree-4-general_options.seed
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fmax=iqtree-4-modelling_parameters.site_specific_frequency.fmax
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.pers=iqtree-4-tree_parameters.tree_search.pers
+pipeline.parameters.qiphylo.iqtree-4-general_options.keep_ident=iqtree-4-general_options.keep_ident
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.mrate=iqtree-4-modelling_parameters.automatic_model.mrate
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.i=iqtree-4-modelling_parameters.rate_heterogeneity.i
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bcor
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.ru=iqtree-4-tree_parameters.generating_random.ru
+pipeline.parameters.qiphylo.iqtree-4-general_options.safe=iqtree-4-general_options.safe
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bo
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zw=iqtree-4-tree_parameters.tree_topology.zw
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.a=iqtree-4-modelling_parameters.rate_heterogeneity.a
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmin=iqtree-4-modelling_parameters.automatic_model.cmin
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.m=iqtree-4-modelling_parameters.automatic_model.cond_model.m
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.merit=iqtree-4-modelling_parameters.automatic_model.merit
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.minsup=iqtree-4-tree_parameters.constructing_consensus.minsup
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nstop=iqtree-4-tree_parameters.tree_search.nstop
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.bc
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.sprrad=iqtree-4-tree_parameters.tree_search.sprrad
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.n=iqtree-4-tree_parameters.tree_search.n
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.site_specific_frequency.fs=iqtree-4-modelling_parameters.site_specific_frequency.fs
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.wsr=iqtree-4-modelling_parameters.rate_heterogeneity.wsr
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbtl
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.au=iqtree-4-tree_parameters.tree_topology.au
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.lmap=iqtree-4-likelihood_mapping.lmap
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_topology.zb=iqtree-4-tree_parameters.tree_topology.zb
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.suptag=iqtree-4-tree_parameters.constructing_consensus.suptag
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.bi=iqtree-4-tree_parameters.constructing_consensus.bi
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nm
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.wbt
+pipeline.parameters.qiphylo.iqtree-4-likelihood_mapping.wql=iqtree-4-likelihood_mapping.wql
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bb
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.madd=iqtree-4-modelling_parameters.automatic_model.madd
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.abayes=iqtree-4-tree_parameters.single_branch.abayes
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv=iqtree-4-modelling_parameters.rate_heterogeneity.opt_gamma_inv
+pipeline.parameters.qiphylo.iqtree-4-general_options.st=iqtree-4-general_options.st
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.bspec
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.partition_model.spp=iqtree-4-modelling_parameters.partition_model.spp
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rlen=iqtree-4-tree_parameters.generating_random.rlen
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ntop=iqtree-4-tree_parameters.tree_search.ntop
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj=iqtree-4-tree_parameters.computing_robinson_foulds.rf_adj
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.beps
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep=iqtree-4-bootstrap_parameters.ultrafast_bootstrap.nstep
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.alrt=iqtree-4-tree_parameters.single_branch.alrt
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.single_branch.lbp=iqtree-4-tree_parameters.single_branch.lbp
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.rate_heterogeneity.gmedian=iqtree-4-modelling_parameters.rate_heterogeneity.gmedian
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.nbest=iqtree-4-tree_parameters.tree_search.nbest
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.net=iqtree-4-tree_parameters.constructing_consensus.net
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.specifying_substitution.mwopt=iqtree-4-modelling_parameters.specifying_substitution.mwopt
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cmax=iqtree-4-modelling_parameters.automatic_model.cmax
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel=iqtree-4-modelling_parameters.automatic_model.cond_model.opt_custommodel
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.generating_random.rcat=iqtree-4-tree_parameters.generating_random.rcat
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.constructing_consensus.con=iqtree-4-tree_parameters.constructing_consensus.con
+pipeline.parameters.qiphylo.iqtree-4-miscellaneous_options.fconst=iqtree-4-miscellaneous_options.fconst
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.allnni=iqtree-4-tree_parameters.tree_search.allnni
+pipeline.parameters.qiphylo.iqtree-4-tree_parameters.tree_search.ninit=iqtree-4-tree_parameters.tree_search.ninit
+pipeline.parameters.qiphylo.iqtree-4-modelling_parameters.automatic_model.msub=iqtree-4-modelling_parameters.automatic_model.msub
+pipeline.parameters.qiphylo.iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b=iqtree-4-bootstrap_parameters.nonparametric_bootstrap.b
