annotate qiime2__diversity__beta_group_significance.xml @ 4:35c850ccce45 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit c7e80dcda727ce63b42aa8a946e9330310929797

<?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: 2024.5.0)
for:
    qiime2 (version: 2024.5.0)
-->
<tool name="qiime2 diversity beta-group-significance" id="qiime2__diversity__beta_group_significance" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
    <description>Beta diversity group significance</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
    </requirements>
    <version_command>q2galaxy version diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity beta_group_significance '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required]  Matrix of distances between pairs of samples.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="DistanceMatrix"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator>
        </param>
        <conditional name="metadata">
            <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required]  Categorical sample metadata column.">
                <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="method" type="select" label="method: Str % Choices('permanova', 'anosim', 'permdisp')" display="radio">
                <option value="permanova" selected="true">permanova</option>
                <option value="anosim">anosim</option>
                <option value="permdisp">permdisp</option>
            </param>
            <param name="pairwise" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="pairwise: Bool" help="[default: No]  Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column."/>
            <param name="permutations" type="integer" value="999" label="permutations: Int" help="[default: 999]  The number of permutations to be run when computing p-values."/>
        </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: diversity beta-group-significance
==========================================
Beta diversity group significance


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

|  

Description:
------------
Determine whether groups of samples are significantly different from one another using a permutation-based statistical test.


|  

</help>
    <citations>
        <citation type="doi">https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>