Update Galaxy Tools (#70)

tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 alignment mafft" id="qiime2__alignment__mafft" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mafft" id="qiime2__alignment__mafft" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>De novo multiple sequence alignment with MAFFT</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mafft '$inputs'</command>

tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Add sequences to multiple sequence alignment with MAFFT.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mafft_add '$inputs'</command>
@@ -36,6 +39,7 @@ for:
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
             <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No]  This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default"/>
             <param name="addfragments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="addfragments: Bool" help="[default: No]  Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used."/>
+            <param name="keeplength" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="keeplength: Bool" help="[default: No]  If selected, the alignment length will be unchanged. Any added sequence that would otherwise introduce new insertions into the alignment, will have those insertions deleted, to preserve original alignment length."/>
         </section>
     </inputs>
     <outputs>

tools/suite_qiime2__alignment/qiime2__alignment__mask.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 alignment mask" id="qiime2__alignment__mask" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mask" id="qiime2__alignment__mask" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Positional conservation and gap filtering.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mask '$inputs'</command>

tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 composition add-pseudocount" id="qiime2__composition__add_pseudocount" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition add-pseudocount" id="qiime2__composition__add_pseudocount" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Add pseudocount to table.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition add_pseudocount '$inputs'</command>

tools/suite_qiime2__composition/qiime2__composition__ancom.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 composition ancom" id="qiime2__composition__ancom" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition ancom" id="qiime2__composition__ancom" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Apply ANCOM to identify features that differ in abundance.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition ancom '$inputs'</command>

tools/suite_qiime2__composition/qiime2__composition__ancombc.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Analysis of Composition of Microbiomes with Bias Correction</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition ancombc '$inputs'</command>

tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 composition da-barplot" id="qiime2__composition__da_barplot" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition da-barplot" id="qiime2__composition__da_barplot" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Differential abundance bar plots</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition da_barplot '$inputs'</command>

tools/suite_qiime2__composition/qiime2__composition__tabulate.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description> View tabular output from ANCOM-BC.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition tabulate '$inputs'</command>

tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Demultiplex paired-end sequence data with barcodes in-sequence.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version cutadapt</version_command>
     <command detect_errors="exit_code">q2galaxy run cutadapt demux_paired '$inputs'</command>

tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 cutadapt demux-single" id="qiime2__cutadapt__demux_single" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt demux-single" id="qiime2__cutadapt__demux_single" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Demultiplex single-end sequence data with barcodes in-sequence.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version cutadapt</version_command>
     <command detect_errors="exit_code">q2galaxy run cutadapt demux_single '$inputs'</command>

tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version cutadapt</version_command>
     <command detect_errors="exit_code">q2galaxy run cutadapt trim_paired '$inputs'</command>

tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 cutadapt trim-single" id="qiime2__cutadapt__trim_single" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt trim-single" id="qiime2__cutadapt__trim_single" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Find and remove adapters in demultiplexed single-end sequences.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version cutadapt</version_command>
     <command detect_errors="exit_code">q2galaxy run cutadapt trim_single '$inputs'</command>

tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate single-end Pacbio CCS</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_ccs '$inputs'</command>
@@ -33,13 +36,23 @@ for:
             </sanitizer>
             <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
         </param>
-        <param name="adapter" type="text" label="adapter: Str" help="[required]  Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded.">
-            <sanitizer>
-                <valid initial="string.printable"/>
-            </sanitizer>
-            <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
-        </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <conditional name="__q2galaxy__GUI__conditional__adapter__" label="adapter: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="adapter: Str" help="[optional]  Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded.">
+                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
+                    <option value="__q2galaxy__::control::provide">Provide a value</option>
+                </param>
+                <when value="__q2galaxy__::control::default">
+                    <param name="adapter" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="adapter" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
             <param name="max_mismatch" type="integer" value="2" label="max_mismatch: Int" help="[default: 2]  The number of mismatches to tolerate when matching reads to primer sequences - see http://benjjneb.github.io/dada2/ for complete details."/>
             <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="indels: Bool" help="[default: No]  Allow insertions or deletions of bases when matching adapters. Note that primer matching can be significantly slower, currently about 4x slower"/>
             <param name="trunc_len" type="integer" value="0" label="trunc_len: Int" help="[default: 0]  Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed. Note: Since Pacbio CCS sequences were normally with very high quality scores, there is no need to truncate the Pacbio CCS sequences."/>

tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml

@@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate paired-end sequences</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_paired '$inputs'</command>