<?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 mantel" id="qiime2__diversity__mantel" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
    <description>Apply the Mantel test to two distance matrices</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 mantel '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="dm1" type="data" format="qza" label="dm1: 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>
        <param name="dm2" type="data" format="qza" label="dm2: 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>
        <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="Distance Matrix 1" label="label1: Str" help="[default: 'Distance Matrix 1']  Label for `dm1` in the output visualization.">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
            <param name="label2" type="text" value="Distance Matrix 2" label="label2: Str" help="[default: 'Distance Matrix 2']  Label for `dm2` in the output visualization.">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
        </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 mantel
=========================
Apply the Mantel test to two distance matrices


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

|  

Description:
------------
Apply a two-sided Mantel test to identify correlation between two distance matrices.

Note: the directionality of the comparison has no bearing on the results. Thus, comparing distance matrix X to distance matrix Y is equivalent to comparing Y to X.

Note: the order of samples within the two distance matrices does not need to be the same; the distance matrices will be reordered before applying the Mantel test.

See the scikit-bio docs for more details about the Mantel test:

http://scikit-bio.org/docs/latest/generated/skbio.stats.distance.mantel


|  

</help>
    <citations>
        <citation type="bibtex">@article{cite1,
 author = {Mantel, Nathan},
 journal = {Cancer research},
 number = {2 Part 1},
 pages = {209--220},
 publisher = {AACR},
 title = {The detection of disease clustering and a generalized regression approach},
 volume = {27},
 year = {1967}
}
</citation>
        <citation type="doi">https://doi.org/10.1098/rspl.1895.0041</citation>
        <citation type="doi">https://doi.org/10.2307/1422689</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>