| Next changeset 1:738ef153dcb1 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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added:
qiime2__longitudinal__nmit.xml test-data/.gitkeep |
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| diff -r 000000000000 -r 6f143d604b84 qiime2__longitudinal__nmit.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__longitudinal__nmit.xml Mon Aug 29 20:10:02 2022 +0000 |
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| @@ -0,0 +1,91 @@ +<?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) > 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> |