Merge pull request #10592 from hexylena/edam-tool-panel

EDAM tool panel

doc/source/admin/galaxy_options.rst

@@ -3227,6 +3227,29 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_beta_edam_toolbox``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Enable beta EDAM organised toolbox which ignores admin managed
+    sections in lieu of EDAM topics only.
+:Default: ``false``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``beta_edam_toolbox_ontology_path``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Sets the path to EDAM ontology file.
+    The value of this option will be resolved with respect to
+    <data_dir>.
+:Default: ``EDAM.tsv``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``default_workflow_export_format``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/config/sample/galaxy.yml.sample

@@ -1612,6 +1612,15 @@ galaxy:
   # workflows built using these modules may not function in the future.)
   #enable_beta_workflow_modules: false
 
+  # Enable beta EDAM organised toolbox which ignores admin managed
+  # sections in lieu of EDAM topics only.
+  #enable_beta_edam_toolbox: false
+
+  # Sets the path to EDAM ontology file.
+  # The value of this option will be resolved with respect to
+  # <data_dir>.
+  #beta_edam_toolbox_ontology_path: EDAM.tsv
+
   # Default format for the export of workflows. Possible values are 'ga'
   # or 'format2'.
   #default_workflow_export_format: ga

lib/galaxy/tools/apply_rules.xml

@@ -3,6 +3,10 @@
       version="1.1.0"
       tool_type="apply_rules_to_collection">
     <type class="ApplyRulesTool" module="galaxy.tools" />
+    <edam_operations>
+        <edam_operation>operation_2409</edam_operation>
+        <edam_operation>operation_3695</edam_operation>
+    </edam_operations>
     <action module="galaxy.tools.actions.model_operations"
             class="ModelOperationToolAction"/>
     <inputs>
@@ -15,14 +19,14 @@
     </outputs>
     <help><![CDATA[
 
-This tool allows one to process an existing Galaxy dataset collection's metadata as tabular data, 
+This tool allows one to process an existing Galaxy dataset collection's metadata as tabular data,
 apply a series of rules to it, and generate a new collection. When used interactively in the tool
 form, a dynamic preview of the processing will be available in a tabular data viewer but this tool
 may be used in workflows as well where no such preview can be generated.
 
 This tool is an advanced feature but has a lot of flexibility - it can be used to process collections
 with arbitrary nesting and can do many kinds of filtering, re-sorting, nesting,
-flattening, and arbitrary combinations thereof not possible with Galaxy's other, more simple 
+flattening, and arbitrary combinations thereof not possible with Galaxy's other, more simple
 collection operation tools.
 
 More information about the rule processor in general can be found `here

lib/galaxy/tools/build_list.xml

@@ -6,6 +6,9 @@
   <type class="BuildListCollectionTool" module="galaxy.tools" />
   <action module="galaxy.tools.actions.model_operations"
           class="ModelOperationToolAction"/>
+  <edam_operations>
+    <edam_operation>operation_2409</edam_operation>
+  </edam_operations>
   <inputs>
     <repeat name="datasets" title="Dataset">
       <param type="data" name="input" optional="true" label="Input Dataset" />

lib/galaxy/tools/data_fetch.xml

@@ -4,6 +4,9 @@
       workflow_compatible="false"
       profile="18.01">
   <action module="galaxy.tools.actions.upload" class="FetchUploadToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_0224</edam_operation>
+    </edam_operations>
   <command><![CDATA[
     python '$__tool_directory__/data_fetch.py'
                 --galaxy-root '$GALAXY_ROOT_DIR'

lib/galaxy/tools/extract_dataset.xml

@@ -6,14 +6,17 @@
   <type class="ExtractDatasetCollectionTool" module="galaxy.tools" />
   <action module="galaxy.tools.actions.model_operations"
           class="ModelOperationToolAction"/>
+  <edam_operations>
+    <edam_operation>operation_3695</edam_operation>
+  </edam_operations>
   <inputs>
     <param type="data_collection" collection_type="list,paired" name="input" label="Input List" />
     <conditional name="which">
       <param name="which_dataset" type="select" label="How should a dataset be selected?">
         <option value="first">The first dataset</option>
         <option value="by_identifier">Select by element identifier</option>
         <option value="by_index">Select by index</option>
-      </param>      
+      </param>
       <when value="first" />
       <when value="by_identifier">
         <param name="identifier" label="Element identifier:" type="text">

lib/galaxy/tools/filter_empty_collection.xml

@@ -6,6 +6,9 @@
     <type class="FilterEmptyDatasetsTool" module="galaxy.tools" />
     <action module="galaxy.tools.actions.model_operations"
             class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_3695</edam_operation>
+    </edam_operations>
     <inputs>
         <param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
     </inputs>

lib/galaxy/tools/filter_failed_collection.xml

@@ -6,6 +6,9 @@
     <type class="FilterFailedDatasetsTool" module="galaxy.tools" />
     <action module="galaxy.tools.actions.model_operations"
             class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_3695</edam_operation>
+    </edam_operations>
     <inputs>
         <param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
     </inputs>

lib/galaxy/tools/filter_from_file.xml

@@ -6,6 +6,9 @@
     <type class="FilterFromFileTool" module="galaxy.tools" />
     <action module="galaxy.tools.actions.model_operations"
             class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_3695</edam_operation>
+    </edam_operations>
     <inputs>
         <param type="data_collection" name="input" label="Input Collection" help="A list whose elements will be filtered."/>
         <conditional name="how">
@@ -78,13 +81,13 @@
         </test>
     </tests>
     <help><![CDATA[
-    
+
 .. class:: infomark
 
-        This tool will take an input list and a text file with  
+        This tool will take an input list and a text file with
         names (i.e. identifiers). It will split the input list into
         two new lists - one filtered to contain only the list members
-        whose names are listed in the text file, and one containing 
+        whose names are listed in the text file, and one containing
         all the other elements.
 
         This tool will create new history datasets from your collection

lib/galaxy/tools/flatten_collection.xml

@@ -6,6 +6,9 @@
     <type class="FlattenTool" module="galaxy.tools" />
     <action module="galaxy.tools.actions.model_operations"
             class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_2409</edam_operation>
+    </edam_operations>
     <inputs>
         <param type="data_collection" name="input" label="Input Collection" />
         <param type="select" name="join_identifier" label="Join collection identifiers using" help="">

lib/galaxy/tools/merge_collection.xml

@@ -6,6 +6,9 @@
   <type class="MergeCollectionTool" module="galaxy.tools" />
   <action module="galaxy.tools.actions.model_operations"
           class="ModelOperationToolAction"/>
+  <edam_operations>
+    <edam_operation>operation_2409</edam_operation>
+  </edam_operations>
   <macros>
       <xml name="suffix_param">
           <param name="suffix_pattern" label="Use the follow suffix pattern:" help="Describe the suffix pattern to use when joing element name and data copy number. For instance, the default is '_#', which will produce _1 as the first suffix used." value="_#" type="text">
@@ -63,7 +66,7 @@
             <option value="keep_first" selected="true">Keep first instance</option>
             <option value="keep_last">Keep last instance</option>
             <option value="fail">Fail collection creation</option>
-          </param>      
+          </param>
           <when value="suffix_conflict">
             <expand macro="suffix_param" />
           </when>
@@ -93,7 +96,7 @@
                 <element name="forward" value="simple_line.txt" />
                 <element name="reverse" value="simple_line_alternative.txt" />
               </collection>
-            </element>          
+            </element>
           </collection>
         </param>
       </repeat>
@@ -105,7 +108,7 @@
                 <element name="forward" value="simple_line.txt" />
                 <element name="reverse" value="simple_line_alternative.txt" />
               </collection>
-            </element>           
+            </element>
           </collection>
         </param>
       </repeat>
@@ -125,7 +128,7 @@
           <element name="reverse">
             <expand macro="assert_is_simple_line_alternative" />
           </element>
-        </element>        
+        </element>
       </output_collection>
     </test>
     <test>
@@ -137,7 +140,7 @@
       <repeat name="inputs">
         <param name="input">
           <expand macro="test_collecton_simple_then_alternative" />
-        </param>      
+        </param>
       </repeat>
       <expand macro="advanced_section" duplicate_handling="suffix_every" suffix_pattern="__#" />
       <output_collection name="output" type="list">
@@ -160,7 +163,7 @@
           <assert_contents>
             <has_text_matching expression="^This is a different line of text.\n$"/>
           </assert_contents>
-        </element>                
+        </element>
       </output_collection>
     </test>
     <test>
@@ -175,7 +178,7 @@
             <element name="sample3" value ="simple_line.txt"/>
             <element name="sample4" value ="simple_line_alternative.txt"/>
           </collection>
-        </param>      
+        </param>
       </repeat>
       <expand macro="advanced_section" duplicate_handling="suffix_every" suffix_pattern="__#" />
       <output_collection name="output" type="list">
@@ -190,7 +193,7 @@
         </element>
         <element name="sample4__2">
             <expand macro="assert_is_simple_line_alternative" />
-        </element>                
+        </element>
       </output_collection>
     </test>
     <test>
@@ -203,7 +206,7 @@
       <repeat name="inputs">
         <param name="input">
           <expand macro="test_collecton_simple_then_alternative" />
-        </param>      
+        </param>
       </repeat>
       <output_collection name="output" type="list">
         <element name="sample1">
@@ -217,7 +220,7 @@
         </element>
         <element name="sample2-2">
             <expand macro="assert_is_simple_line_alternative" />
-        </element>                
+        </element>
       </output_collection>
     </test>
     <test>
@@ -229,7 +232,7 @@
       <repeat name="inputs">
         <param name="input">
           <expand macro="test_collection_alternative_then_simple" />
-        </param>      
+        </param>
       </repeat>
       <output_collection name="output" type="list">
         <element name="sample1">
@@ -273,7 +276,7 @@
   <help><![CDATA[
 
 This tool takes two lists and creates a single unified list.
-    
+
 .. class:: infomark
 
 This tool will create new history datasets for your collection but your quota usage will not increase.

lib/galaxy/tools/relabel_from_file.xml

@@ -6,6 +6,9 @@
     <type class="RelabelFromFileTool" module="galaxy.tools" />
     <action module="galaxy.tools.actions.model_operations"
             class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_3096</edam_operation>
+    </edam_operations>
     <inputs>
         <param type="data_collection" name="input" label="Input Collection" help="A list whose identifiers will be relabelled."/>
         <conditional name="how">
@@ -133,7 +136,7 @@
         </test>
     </tests>
     <help><![CDATA[
-    
+
 .. class:: infomark
 
         This tool will take an input list and a text file with new identifiers
@@ -147,8 +150,8 @@
         in the collection. In that case only matching list identifiers will be
         relabeled.
 
-        Valid identifiers must contain only characters (a-z, A-Z), numbers (0-9), 
-        dash and underscore (-, _). Punctuation or whitespace are not allowed. 
+        Valid identifiers must contain only characters (a-z, A-Z), numbers (0-9),
+        dash and underscore (-, _). Punctuation or whitespace are not allowed.
 
         This tool will create new history datasets from your collection
         but your quota usage will not increase.

lib/galaxy/tools/sort_collection_list.xml

@@ -6,6 +6,9 @@
     <type class="SortTool" module="galaxy.tools" />
     <action module="galaxy.tools.actions.model_operations"
             class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_3802</edam_operation>
+    </edam_operations>
     <inputs>
         <param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
         <conditional name="sort_type">

lib/galaxy/tools/tag_collection_from_file.xml

@@ -6,6 +6,9 @@
     <type class="TagFromFileTool" module="galaxy.tools" />
     <action module="galaxy.tools.actions.model_operations"
             class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_3096</edam_operation>
+    </edam_operations>
     <inputs>
         <param type="data_collection" name="input" label="Input Collection" help="A tabular file indicating how to tag collection elements."/>
         <param type="data" name="tags" format="tabular" label="Tag collection elements according to this file"/>