<?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: 2024.2.1)
for:
    qiime2 (version: 2024.2.0)
-->
<tool name="qiime2 diversity procrustes-analysis" id="qiime2__diversity__procrustes_analysis" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Procrustes Analysis</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity procrustes_analysis '$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>
        <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"/>
            <conditional name="__q2galaxy__GUI__conditional__permutations__">
                <param name="__q2galaxy__GUI__select__" type="select" label="permutations: Int % Range(1, None) | Str % Choices('disable')" help="[default: 999]  The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired).">
                    <option value="disable">disable (Str)</option>
                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
                </param>
                <when value="disable">
                    <param name="permutations" type="hidden" value="disable"/>
                </when>
                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
                    <param name="permutations" type="integer" min="1" value="999" label="permutations: Int % Range(1, None)" help="[default: 999]  The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired)."/>
                </when>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="transformed_reference" format="qza" label="${tool.name} on ${on_string}: transformed_reference.qza" from_work_dir="transformed_reference.qza"/>
        <data name="transformed_other" format="qza" label="${tool.name} on ${on_string}: transformed_other.qza" from_work_dir="transformed_other.qza"/>
        <data name="disparity_results" format="qza" label="${tool.name} on ${on_string}: disparity_results.qza" from_work_dir="disparity_results.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: diversity procrustes-analysis
======================================
Procrustes Analysis


Outputs:
--------
:transformed_reference.qza: A normalized version of the "reference" ordination matrix.
:transformed_other.qza: A normalized and fitted version of the "other" ordination matrix.
:disparity_results.qza: The sum of the squares of the pointwise differences between the two input datasets &amp; its p value.

|  

Description:
------------
Fit two ordination matrices with Procrustes analysis


|  

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