# HG changeset patch
# User q2d2
# Date 1686253958 0
# Node ID 124673b2e9e7207e26902c09799344a8bcc5676a
# Parent  5750bac5b7443abc9c88e165a1b46b892b27c0cf
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 65e4952f33eb335528e8553150e9097e5ea8f556

diff -r 5750bac5b744 -r 124673b2e9e7 qiime2__taxa__barplot.xml
--- a/qiime2__taxa__barplot.xml	Fri Jan 13 23:01:20 2023 +0000
+++ b/qiime2__taxa__barplot.xml	Thu Jun 08 19:52:38 2023 +0000
@@ -6,14 +6,14 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2022.11.1)
+    q2galaxy (version: 2023.5.0)
 for:
-    qiime2 (version: 2022.11.1)
+    qiime2 (version: 2023.5.1)
 -->
-<tool name="qiime2 taxa barplot" id="qiime2__taxa__barplot" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 taxa barplot" id="qiime2__taxa__barplot" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
     <description>Visualize taxonomy with an interactive bar plot</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.11</container>
+        <container type="docker">quay.io/qiime2/core:2023.5</container>
     </requirements>
     <version_command>q2galaxy version taxa</version_command>
     <command detect_errors="exit_code">q2galaxy run taxa barplot '$inputs'</command>
@@ -21,19 +21,20 @@
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
     <inputs>
-        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  Feature table to visualize at various taxonomic levels.">
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | PresenceAbsence]" help="[required]  Feature table to visualize at various taxonomic levels.">
             <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
             </options>
-            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
-        </param>
-        <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required]  Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.">
-            <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureData[Taxonomy]"/>
-            </options>
-            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]']</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: FeatureData[Taxonomy]" help="[optional]  Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. If no taxonomy is provided, the feature IDs will be used as labels.">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="FeatureData[Taxonomy]"/>
+                </options>
+                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
+            </param>
             <repeat name="metadata" help="[optional]  The sample metadata." title="metadata: Metadata">
                 <conditional name="__q2galaxy__GUI__conditional__metadata__">
                     <param name="type" type="select" label="metadata: Metadata">
@@ -48,6 +49,22 @@
                     </when>
                 </conditional>
             </repeat>
+            <conditional name="__q2galaxy__GUI__conditional__level_delimiter__" label="level_delimiter: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="level_delimiter: Str" help="[optional]  Attempt to parse hierarchical taxonomic information from feature IDs by separating levels with this character. This parameter is ignored if a taxonomy is provided as input.">
+                    <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="level_delimiter" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="level_delimiter" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
         </section>
     </inputs>
     <outputs>
@@ -95,15 +112,15 @@
 *******
 Using the ``qiime2 taxa barplot`` tool:
  #. Set *"table"* to ``#: table.qza``
- #. Set *"taxonomy"* to ``#: taxonomy.qza``
  #. Expand the ``additional options`` section
 
-    - For *"metadata"*:
+    #. Set *"taxonomy"* to ``#: taxonomy.qza``
+    #. For *"metadata"*:
 
-      - Press the ``+ Insert metadata`` button to set up the next steps.
+       - Press the ``+ Insert metadata`` button to set up the next steps.
 
-        #. Leave as ``Metadata from TSV``
-        #. Set *"Metadata Source"* to ``sample-metadata.tsv``
+         #. Leave as ``Metadata from TSV``
+         #. Set *"Metadata Source"* to ``sample-metadata.tsv``
 
 
 
diff -r 5750bac5b744 -r 124673b2e9e7 test-data/barplot.test0.table.qza
Binary file test-data/barplot.test0.table.qza has changed
diff -r 5750bac5b744 -r 124673b2e9e7 test-data/barplot.test0.taxonomy.qza
Binary file test-data/barplot.test0.taxonomy.qza has changed
diff -r 5750bac5b744 -r 124673b2e9e7 test-data/collapse.test0.table.qza
Binary file test-data/collapse.test0.table.qza has changed
diff -r 5750bac5b744 -r 124673b2e9e7 test-data/collapse.test0.taxonomy.qza
Binary file test-data/collapse.test0.taxonomy.qza has changed