# HG changeset patch
# User q2d2
# Date 1661803174 0
# Node ID 5e6afe86c5b8a64ded4223f5d7437e3ec6610125

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

diff -r 000000000000 -r 5e6afe86c5b8 qiime2__feature_table__rename_ids.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__feature_table__rename_ids.xml	Mon Aug 29 19:59:34 2022 +0000
@@ -0,0 +1,86 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2022, 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)
+for:
+    qiime2 (version: 2022.8.1)
+-->
+<tool name="qiime2 feature-table rename-ids" id="qiime2__feature_table__rename_ids" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Renames sample or feature ids in a table</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version feature_table</version_command>
+    <command detect_errors="aggressive">q2galaxy run feature_table rename_ids '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required]  The table to be renamed">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Composition]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
+        </param>
+        <conditional name="metadata">
+            <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required]  A metadata column defining the new ids. Each original id must map to a new unique id. If strict mode is used, then every id in the original table must have a new id.">
+                <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"/>
+                <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
+                    <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
+                </param>
+            </when>
+            <when value="qza">
+                <param name="source" type="data" format="qza" label="Metadata Source"/>
+                <param name="column" type="text" label="Column Name">
+                    <validator type="empty_field"/>
+                </param>
+            </when>
+        </conditional>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="axis" type="select" label="axis: Str % Choices('feature', 'sample')" display="radio">
+                <option value="feature">feature</option>
+                <option value="sample" selected="true">sample</option>
+            </param>
+            <param name="strict" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="strict: Bool" help="[default: No]  Whether the naming needs to be strict (each id in the table must have a new id). Otherwise, only the ids described in `metadata` will be renamed and the others will keep their original id names."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="renamed_table" format="qza" label="${tool.name} on ${on_string}: renamed_table.qza" from_work_dir="renamed_table.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: feature-table rename-ids
+=================================
+Renames sample or feature ids in a table
+
+
+Outputs:
+--------
+:renamed_table.qza: A table which has new ids, where the ids are replaced by values in the `metadata` column.
+
+|  
+
+Description:
+------------
+Renames the sample or feature ids in a feature table using metadata to define the new ids.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
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