annotate qiime2__diversity__pcoa_biplot.xml @ 7:a262d3792cd2 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9436cc47c72b58a6a3d3a5c2ee075689c2926ef0

<?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: 2025.7.0)
for:
    qiime2 (version: 2025.7.0)
-->
<tool name="qiime2 diversity pcoa-biplot" id="qiime2__diversity__pcoa_biplot" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause">
    <description>Principal Coordinate Analysis Biplot</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
    </requirements>
    <version_command>q2galaxy version diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity pcoa_biplot '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="pcoa" type="data" format="qza" label="pcoa: PCoAResults" help="[required]  The PCoA where the features will be projected onto.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="PCoAResults"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator>
        </param>
        <param name="features" type="data" format="qza" label="features: FeatureTable[RelativeFrequency]" help="[required]  Variables to project onto the PCoA matrix">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator>
        </param>
    </inputs>
    <outputs>
        <data name="biplot" format="qza" label="${tool.name} on ${on_string}: biplot.qza" from_work_dir="biplot.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: diversity pcoa-biplot
==============================
Principal Coordinate Analysis Biplot


Outputs:
--------
:biplot.qza: The resulting PCoA matrix.

|  

Description:
------------
Project features into a principal coordinates matrix. The features used should be the features used to compute the distance matrix. It is recommended that these variables be normalized in cases of dimensionally heterogeneous physical variables.


|  

</help>
    <citations>
        <citation type="bibtex">@inbook{cite1,
 author = {Pierre Legendre and Louis Legendre},
 edition = {Third},
 isbn = {0444-89249},
 pages = {499},
 publisher = {Elsevier},
 title = {Numerical Ecology},
 year = {2012}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>