diff qiime2__feature_table__summarize.xml @ 1:c7553080ec2e draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:52:35 +0000
parents bfe9f18ac641
children 365ce7a8e641
line wrap: on
line diff
--- a/qiime2__feature_table__summarize.xml	Mon Aug 29 20:00:26 2022 +0000
+++ b/qiime2__feature_table__summarize.xml	Fri Jan 13 22:52:35 2023 +0000
@@ -1,31 +1,31 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2022, QIIME 2 development team.
+Copyright (c) 2023, 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: 2022.8.1)
+    q2galaxy (version: 2022.11.1)
 for:
-    qiime2 (version: 2022.8.1)
+    qiime2 (version: 2022.11.1)
 -->
-<tool name="qiime2 feature-table summarize" id="qiime2__feature_table__summarize" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 feature-table summarize" id="qiime2__feature_table__summarize" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Summarize table</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.8</container>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
     </requirements>
     <version_command>q2galaxy version feature_table</version_command>
-    <command detect_errors="aggressive">q2galaxy run feature_table summarize '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run feature_table summarize '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table to be summarized.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
@@ -49,7 +49,18 @@
     <outputs>
         <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="table" value="summarize.test0.feature-table.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 summarize
 ================================
@@ -66,6 +77,27 @@
 ------------
 Generate visual and tabular summaries of a feature table.
 
+Examples:
+---------
+
+feature_table_summarize
+***********************
+Using the ``qiime2 feature-table summarize`` tool:
+ #. Set *"table"* to ``#: feature-table.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 summarize [...] : visualization.qzv``
+      - ``table.qzv``
+
 
 |