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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit c7e80dcda727ce63b42aa8a946e9330310929797
author | q2d2 |
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date | Mon, 03 Jun 2024 23:19:09 +0000 |
parents | 525d07dd31b2 |
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<?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 beta" id="qiime2__diversity__beta" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> <description>Beta diversity</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 beta '$inputs'</command> <configfiles> <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples over which beta diversity should be computed."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureTable[Frequency]"/> <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> </param> <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'braycurtis', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')"> <option value="__q2galaxy__::literal::None">Selection required</option> <option value="aitchison">aitchison</option> <option value="braycurtis">braycurtis</option> <option value="canberra">canberra</option> <option value="canberra_adkins">canberra_adkins</option> <option value="chebyshev">chebyshev</option> <option value="cityblock">cityblock</option> <option value="correlation">correlation</option> <option value="cosine">cosine</option> <option value="dice">dice</option> <option value="euclidean">euclidean</option> <option value="hamming">hamming</option> <option value="jaccard">jaccard</option> <option value="jensenshannon">jensenshannon</option> <option value="matching">matching</option> <option value="minkowski">minkowski</option> <option value="rogerstanimoto">rogerstanimoto</option> <option value="russellrao">russellrao</option> <option value="seuclidean">seuclidean</option> <option value="sokalmichener">sokalmichener</option> <option value="sokalsneath">sokalsneath</option> <option value="sqeuclidean">sqeuclidean</option> <option value="yule">yule</option> <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> </param> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> <param name="pseudocount" type="integer" min="1" value="1" label="pseudocount: Int % Range(1, None)" help="[default: 1] A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics."/> </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: diversity beta ======================= Beta diversity Outputs: -------- :distance_matrix.qza: The resulting distance matrix. | Description: ------------ Computes a user-specified beta diversity metric for all pairs of samples in a feature table. | </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>