# HG changeset patch
# User q2d2
# Date 1714079505 0
# Node ID 2feea4c63f4c2532a24e12c528aca96929f877f3
# Parent  6d5cd7bcc0d05de326328ff128c3b41460c66240
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c qiime2__feature_table__tabulate_seqs.xml
--- a/qiime2__feature_table__tabulate_seqs.xml	Thu Jun 08 19:44:24 2023 +0000
+++ b/qiime2__feature_table__tabulate_seqs.xml	Thu Apr 25 21:11:45 2024 +0000
@@ -1,33 +1,59 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 feature-table tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 feature-table tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>View sequence associated with each feature</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version feature_table</version_command>
     <command detect_errors="exit_code">q2galaxy run feature_table tabulate_seqs '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="data" type="data" format="qza" label="data: FeatureData[Sequence | AlignedSequence]" help="[required]  The feature sequences to be tabulated.">
             <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
                 <filter type="add_value" value="FeatureData[Sequence]"/>
-                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator>
         </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="taxonomy" type="data" format="qza" optional="true" label="taxonomy: Collection[FeatureData[Taxonomy]]" help="[optional]  The taxonomic classifications of the tabulated features." multiple="true">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="FeatureData[Taxonomy]"/>
+                </options>
+            </param>
+            <repeat name="metadata" help="[optional]  Any additional metadata for the tabulated features." title="metadata: Metadata">
+                <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                    <param name="type" type="select" label="metadata: Metadata">
+                        <option value="tsv" selected="true">Metadata from TSV</option>
+                        <option value="qza">Metadata from Artifact</option>
+                    </param>
+                    <when value="tsv">
+                        <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
+                    </when>
+                    <when value="qza">
+                        <param name="source" type="data" format="qza" label="Metadata Source"/>
+                    </when>
+                </conditional>
+            </repeat>
+            <param name="merge_method" type="select" label="merge_method: Str % Choices('strict', 'union', 'intersect')" display="radio">
+                <option value="strict" selected="true">strict</option>
+                <option value="union">union</option>
+                <option value="intersect">intersect</option>
+            </param>
+        </section>
     </inputs>
     <outputs>
         <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
@@ -43,6 +69,28 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="data" value="tabulate_seqs.test1.rep-seqs-single-taxon.qza" ftype="qza"/>
+            <param name="taxonomy" value="tabulate_seqs.test1.single-taxonomy.qza" ftype="qza"/>
+            <output name="visualization" ftype="qzv">
+                <assert_contents>
+                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+                        <has_line_matching expression="type: Visualization"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data" value="tabulate_seqs.test2.rep-seqs-multi-taxon.qza" ftype="qza"/>
+            <param name="taxonomy" value="tabulate_seqs.test2.multi-taxonomy/GG1.qza,tabulate_seqs.test2.multi-taxonomy/GG2.qza" ftype="qza"/>
+            <output name="visualization" ftype="qzv">
+                <assert_contents>
+                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+                        <has_line_matching expression="type: Visualization"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 QIIME 2: feature-table tabulate-seqs
@@ -81,6 +129,50 @@
     * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
       - ``rep-seqs.qzv``
 
+feature_table_tabulate_seqs_single_taxon
+****************************************
+Using the ``qiime2 feature-table tabulate-seqs`` tool:
+ #. Set *"data"* to ``#: rep-seqs-single-taxon.qza``
+ #. Expand the ``additional options`` section
+
+    - Set *"taxonomy"* to ``#: ['single-taxonomy.qza']``
+
+ #. Press the ``Execute`` button.
+
+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+    :align: left
+    :header-rows: 1
+
+    * - History Name
+      - *"Name"* to set (be sure to press ``Save``)
+    * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
+      - ``rep-seqs.qzv``
+
+feature_table_tabulate_seqs_multi_taxon
+***************************************
+Using the ``qiime2 feature-table tabulate-seqs`` tool:
+ #. Set *"data"* to ``#: rep-seqs-multi-taxon.qza``
+ #. Expand the ``additional options`` section
+
+    - Set *"taxonomy"* to ``#: multi-taxonomy/``
+
+ #. Press the ``Execute`` button.
+
+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+    :align: left
+    :header-rows: 1
+
+    * - History Name
+      - *"Name"* to set (be sure to press ``Save``)
+    * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
+      - ``rep-seqs.qzv``
+
 
 |  
 
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diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c test-data/group.test0.feature-table.qza
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diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c test-data/merge.test0.feature-table1.qza
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diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c test-data/merge.test1.feature-table1.qza
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diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c test-data/merge_seqs.test0.seqs1.qza
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diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c test-data/tabulate_feature_frequencies.test0.feature-table.qza
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diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c test-data/tabulate_seqs.test0.rep-seqs.qza
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diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c test-data/tabulate_seqs.test1.rep-seqs-single-taxon.qza
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diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c test-data/tabulate_seqs.test1.single-taxonomy.qza
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diff -r 6d5cd7bcc0d0 -r 2feea4c63f4c test-data/tabulate_seqs.test2.multi-taxonomy/.order
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabulate_seqs.test2.multi-taxonomy/.order	Thu Apr 25 21:11:45 2024 +0000
@@ -0,0 +1,2 @@
+GG1
+GG2
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