annotate qiime2__diversity__alpha_group_significance.xml @ 5:96988c25ca01 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 5f71b597c9495eae67a447744fded834f56ca1f7

<?xml version='1.0' encoding='utf-8'?>
<!--
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: 2024.10.0)
for:
    qiime2 (version: 2024.10.1)
-->
<tool name="qiime2 diversity alpha-group-significance" id="qiime2__diversity__alpha_group_significance" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Alpha diversity comparisons</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
    </requirements>
    <version_command>q2galaxy version diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity alpha_group_significance '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="alpha_diversity" type="data" format="qza" label="alpha_diversity: SampleData[AlphaDiversity]" help="[required]  Vector of alpha diversity values by sample.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="SampleData[AlphaDiversity]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[AlphaDiversity]']</validator>
        </param>
        <repeat name="metadata" min="1" help="[required]  The sample metadata." title="metadata: Metadata">
            <conditional name="__q2galaxy__GUI__conditional__metadata__">
                <param name="type" type="select" label="metadata: Metadata">
                    <option value="tsv" selected="true">Metadata from TSV</option>
                    <option value="qza">Metadata from Artifact</option>
                </param>
                <when value="tsv">
                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                </when>
                <when value="qza">
                    <param name="source" type="data" format="qza" label="Metadata Source"/>
                </when>
            </conditional>
        </repeat>
    </inputs>
    <outputs>
        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests>
        <test>
            <param name="alpha_diversity" value="alpha_group_significance.test0.alpha-div-faith-pd.qza" ftype="qza"/>
            <repeat name="metadata">
                <conditional name="__q2galaxy__GUI__conditional__metadata__">
                    <param name="type" value="tsv"/>
                    <param name="source" value="alpha_group_significance.test0.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <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: diversity alpha-group-significance
===========================================
Alpha diversity comparisons


Outputs:
--------
:visualization.qzv: &lt;no description&gt;

|  

Description:
------------
Visually and statistically compare groups of alpha diversity values.

Examples:
---------

alpha_group_significance_faith_pd
*********************************
Using the ``qiime2 diversity alpha-group-significance`` tool:
 #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza``
 #. For *"metadata"*:

    - Perform the following steps.

      #. Leave as ``Metadata from TSV``
      #. Set *"Metadata Source"* to ``metadata.tsv``


 #. Press the ``Execute`` button.



|  

</help>
    <citations>
        <citation type="doi">10.1080/01621459.1952.10483441</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>