annotate qiime2__stats__alpha_group_significance.xml @ 0:d6f4c80a29a2 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats 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 stats alpha-group-significance" id="qiime2__stats__alpha_group_significance" version="0+unknown-q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Alpha group significance test and plot</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 stats</version_command>
    <command detect_errors="exit_code">q2galaxy run stats 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]  Alpha diversity which will become the &quot;measure&quot;">
            <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]  Sample metadata to use" 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>
        <repeat name="columns" min="1" help="[required]  Columns to include as group information" title="columns: List[Str]">
            <param name="element" type="text" label="element: Str" help="[required]">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
                <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
            </param>
        </repeat>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <conditional name="__q2galaxy__GUI__conditional__subject__">
                <param name="__q2galaxy__GUI__select__" type="select" label="subject: Str % Choices('')¹'³ | Str²'⁴" help="[default: '']  If provided, will cause the results to be matched for repeated measures.">
                    <option value="" selected="true"> (Str)</option>
                    <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>
                    <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>
                </param>
                <when value="">
                    <param name="subject" type="hidden" value=""/>
                </when>
                <when value="__q2galaxy__::control::Str">
                    <param name="subject" type="text" value="" label="subject: Str" help="[default: '']  If provided, will cause the results to be matched for repeated measures.">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
                <when value="__q2galaxy__::control::Str">
                    <param name="subject" type="text" value="" label="subject: Str" help="[default: '']  If provided, will cause the results to be matched for repeated measures.">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <conditional name="__q2galaxy__GUI__conditional__timepoint__">
                <param name="__q2galaxy__GUI__select__" type="select" label="timepoint: Str % Choices('')¹'² | Str³'⁴" help="[default: '']  If provided, will cause the results to be stratified by timepoint. Required if using ``subject``.">
                    <option value="" selected="true"> (Str)</option>
                    <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>
                    <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>
                </param>
                <when value="">
                    <param name="timepoint" type="hidden" value=""/>
                </when>
                <when value="__q2galaxy__::control::Str">
                    <param name="timepoint" type="text" value="" label="timepoint: Str" help="[default: '']  If provided, will cause the results to be stratified by timepoint. Required if using ``subject``.">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
                <when value="__q2galaxy__::control::Str">
                    <param name="timepoint" type="text" value="" label="timepoint: Str" help="[default: '']  If provided, will cause the results to be stratified by timepoint. Required if using ``subject``.">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="distribution" format="qza" label="${tool.name} on ${on_string}: distribution.qza" from_work_dir="distribution.qza"/>
        <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/>
        <data name="raincloud" format="qzv" label="${tool.name} on ${on_string}: raincloud.qzv" from_work_dir="raincloud.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>
            <repeat name="columns">
                <param name="element" value="genotype"/>
            </repeat>
            <repeat name="columns">
                <param name="element" value="donor_status"/>
            </repeat>
            <conditional name="__q2galaxy__GUI__conditional__subject__">
                <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Str"/>
                <param name="subject" value="mouse_id"/>
            </conditional>
            <conditional name="__q2galaxy__GUI__conditional__timepoint__">
                <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Str"/>
                <param name="timepoint" value="days_post_transplant"/>
            </conditional>
            <output name="distribution" ftype="qza">
                <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: Dist1D\[NestedOrdered,\ Matched\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
            <output name="stats" ftype="qza"/>
            <output name="raincloud" ftype="qzv"/>
            <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>
            <repeat name="columns">
                <param name="element" value="genotype"/>
            </repeat>
            <repeat name="columns">
                <param name="element" value="donor_status"/>
            </repeat>
            <output name="distribution" ftype="qza">
                <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: Dist1D\[Multi,\ Independent\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
            <output name="stats" ftype="qza"/>
            <output name="raincloud" ftype="qzv"/>
        </test>
    </tests>
    <help>
QIIME 2: stats alpha-group-significance
=======================================
Alpha group significance test and plot


Outputs:
--------
:distribution.qza: Dist1D generated by metadata and alpha diversity.
:stats.qza: A stats table of the per-group/timepoint results
:raincloud.qzv: A visualization of the distribution and statistics

|  

Description:
------------
Will select between Wilcoxon SRT and Mann-Whitney U depending on the presence of repeated measures.

Examples:
---------

alpha_group_significance_faith_pd
*********************************
Using the ``qiime2 stats 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``


 #. For *"columns"*, use the ``+ columns`` button to add the corresponding values:

    #. Add *"element"* set to ``genotype``
    #. Add *"element"* set to ``donor_status``

 #. Expand the ``additional options`` section

    #. Set *"subject"* to ``mouse_id``
    #. Set *"timepoint"* to ``days_post_transplant``

 #. Press the ``Execute`` button.

Once completed, for each 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 stats alpha-group-significance [...] : distribution.qza``
      - ``dist.qza``
    * - ``#: qiime2 stats alpha-group-significance [...] : stats.qza``
      - ``stats.qza``
    * - ``#: qiime2 stats alpha-group-significance [...] : raincloud.qzv``
      - ``raincloud.qzv``

Using the ``qiime2 stats 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``


 #. For *"columns"*, use the ``+ columns`` button to add the corresponding values:

    #. Add *"element"* set to ``genotype``
    #. Add *"element"* set to ``donor_status``

 #. Press the ``Execute`` button.

Once completed, for each 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 stats alpha-group-significance [...] : distribution.qza``
      - ``dist2.qza``
    * - ``#: qiime2 stats alpha-group-significance [...] : stats.qza``
      - ``stats2.qza``
    * - ``#: qiime2 stats alpha-group-significance [...] : raincloud.qzv``
      - ``raincloud2.qzv``


|  

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