annotate qiime2__diversity__partial_procrustes.xml @ 1:f7b6b5e86608 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 partial-procrustes" id="qiime2__diversity__partial_procrustes" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
    <description>Partial Procrustes</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 partial_procrustes '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="reference" type="data" format="qza" label="reference: PCoAResults" help="[required]  The ordination matrix to which data is fitted to.">
            <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="other" type="data" format="qza" label="other: PCoAResults" help="[required]  The ordination matrix that's fitted to the reference ordination.">
            <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>
        <conditional name="pairing">
            <param name="type" type="select" label="pairing: MetadataColumn[Categorical]" help="[required]  The metadata column describing sample pairs which exist.">
                <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="dimensions" type="integer" min="1" value="5" label="dimensions: Int % Range(1, None)" help="[default: 5]  The number of dimensions to use when fitting the two matrices"/>
        </section>
    </inputs>
    <outputs>
        <data name="transformed" format="qza" label="${tool.name} on ${on_string}: transformed.qza" from_work_dir="transformed.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: diversity partial-procrustes
=====================================
Partial Procrustes


Outputs:
--------
:transformed.qza: The 'other' ordination transformed into the space of the reference ordination.

|  

Description:
------------
Transform one ordination into another, using paired samples to anchor the transformation. This method allows does not require all samples to be paired.


|  

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