<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2023, 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: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 diversity beta-correlation" id="qiime2__diversity__beta_correlation" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Beta diversity correlation</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version diversity</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity beta_correlation '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </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[Numeric]" help="[required]  Numeric metadata column from which to compute pairwise Euclidean distances">
                <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('spearman', 'pearson')" display="radio">
                <option value="spearman" selected="true">spearman</option>
                <option value="pearson">pearson</option>
            </param>
            <param name="permutations" type="integer" min="0" value="999" label="permutations: Int % Range(0, None)" help="[default: 999]  The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired)."/>
            <param name="intersect_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="intersect_ids: Bool" help="[default: No]  If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs."/>
            <param name="label1" type="text" value="Metadata" label="label1: Str" help="[default: 'Metadata']  Label for `distance_matrix` in the output visualization.">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
            <param name="label2" type="text" value="Distance Matrix" label="label2: Str" help="[default: 'Distance Matrix']  Label for `metadata_distance_matrix` in the output visualization.">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="metadata_distance_matrix" format="qza" label="${tool.name} on ${on_string}: metadata_distance_matrix.qza" from_work_dir="metadata_distance_matrix.qza"/>
        <data name="mantel_scatter_visualization" format="qzv" label="${tool.name} on ${on_string}: mantel_scatter_visualization.qzv" from_work_dir="mantel_scatter_visualization.qzv"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: diversity beta-correlation
===================================
Beta diversity correlation


Outputs:
--------
:metadata_distance_matrix.qza: The Distance Matrix produced from the metadata column and used in the mantel test
:mantel_scatter_visualization.qzv: Scatter plot rendering of the manteltest results

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Description:
------------
Create a distance matrix from a numeric metadata column and apply a two-sided Mantel test to identify correlation between two distance matrices. Actions used internally: `distance-matrix` from q2-metadata and `mantel` from q2-diversity.


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