annotate qiime2__stats__prep_alpha_distribution.xml @ 3:3bd5cc9912b2 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.10.0)
for:
    qiime2 (version: 2025.10.0)
-->
<tool name="qiime2 stats prep-alpha-distribution" id="qiime2__stats__prep_alpha_distribution" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Alpha diversity to Dist1D</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
    </requirements>
    <version_command>q2galaxy version stats</version_command>
    <command detect_errors="exit_code">q2galaxy run stats prep_alpha_distribution '$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 Dist1D 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 Dist1D 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 Dist1D 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 Dist1D 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 Dist1D 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 Dist1D 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"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: stats prep-alpha-distribution
======================================
Alpha diversity to Dist1D


Outputs:
--------
:distribution.qza: The resulting Dist1D.

|  

Description:
------------
Alpha diversity to Dist1D


|  

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