diff qiime2__composition__ancom.xml @ 0:cba57f5ca371 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__composition__ancom.xml	Mon Aug 29 19:20:05 2022 +0000
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+<?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 composition ancom" id="qiime2__composition__ancom" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Apply ANCOM to identify features that differ in abundance.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version composition</version_command>
+    <command detect_errors="aggressive">q2galaxy run composition ancom '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Composition]" help="[required]  The feature table to be used for ANCOM computation.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Composition]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]']</validator>
+        </param>
+        <conditional name="metadata">
+            <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required]  The categorical sample metadata column to test for differential abundance across.">
+                <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="transform_function" type="select" label="transform_function: Str % Choices('sqrt', 'log', 'clr')" display="radio">
+                <option value="sqrt">sqrt</option>
+                <option value="log">log</option>
+                <option value="clr" selected="true">clr</option>
+            </param>
+            <param name="difference_function" type="select" label="difference_function: Str % Choices('mean_difference', 'f_statistic')" display="radio">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="mean_difference">mean_difference</option>
+                <option value="f_statistic">f_statistic</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: composition ancom
+==========================
+Apply ANCOM to identify features that differ in abundance.
+
+
+Outputs:
+--------
+:visualization.qzv: &lt;no description&gt;
+
+|  
+
+Description:
+------------
+Apply Analysis of Composition of Microbiomes (ANCOM) to identify features that are differentially abundant across groups.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.3402/mehd.v26.27663</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>