view qiime2__longitudinal__nmit.xml @ 0:6f143d604b84 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2022, 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: 2022.8.1)
for:
    qiime2 (version: 2022.8.1)
-->
<tool name="qiime2 longitudinal nmit" id="qiime2__longitudinal__nmit" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Nonparametric microbial interdependence test</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version longitudinal</version_command>
    <command detect_errors="aggressive">q2galaxy run longitudinal nmit '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[RelativeFrequency]" help="[required]  Feature table to use for microbial interdependence test.">
            <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>
        <repeat name="metadata" min="1" help="[required]  Sample metadata file containing individual_id_column." title="metadata: Metadata">
            <conditional name="__q2galaxy__GUI__conditional__metadata__">
                <param name="type" type="select" label="metadata: Metadata">
                    <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"/>
                </when>
                <when value="qza">
                    <param name="source" type="data" format="qza" label="Metadata Source"/>
                </when>
            </conditional>
        </repeat>
        <param name="individual_id_column" type="text" label="individual_id_column: Str" help="[required]  Metadata column containing IDs for individual subjects.">
            <sanitizer>
                <valid initial="string.printable"/>
            </sanitizer>
            <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="corr_method" type="select" label="corr_method: Str % Choices('kendall', 'pearson', 'spearman')" display="radio">
                <option value="kendall" selected="true">kendall</option>
                <option value="pearson">pearson</option>
                <option value="spearman">spearman</option>
            </param>
            <param name="dist_method" type="select" label="dist_method: Str % Choices('fro', 'nuc')" display="radio">
                <option value="fro" selected="true">fro</option>
                <option value="nuc">nuc</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: longitudinal nmit
==========================
Nonparametric microbial interdependence test


Outputs:
--------
:distance_matrix.qza: The resulting distance matrix.

|  

Description:
------------
Perform nonparametric microbial interdependence test to determine longitudinal sample similarity as a function of temporal microbial composition. For more details and citation, please see doi.org/10.1002/gepi.22065


|  

</help>
    <citations>
        <citation type="doi">10.1002/gepi.22065</citation>
        <citation type="doi">10.1128/mSystems.00219-18</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>