Mercurial > repos > q2d2 > qiime2__diversity__alpha_correlation
view qiime2__diversity__alpha_correlation.xml @ 3:41a4f9caafaa draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author | q2d2 |
---|---|
date | Thu, 25 Apr 2024 20:57:45 +0000 |
parents | 5850f79a2b9f |
children | 339546317bfa |
line wrap: on
line source
<?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: 2024.2.1) for: qiime2 (version: 2024.2.0) --> <tool name="qiime2 diversity alpha-correlation" id="qiime2__diversity__alpha_correlation" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Alpha diversity correlation</description> <requirements> <container type="docker">quay.io/qiime2/amplicon:2024.2</container> </requirements> <version_command>q2galaxy version diversity</version_command> <command detect_errors="exit_code">q2galaxy run diversity alpha_correlation '$inputs'</command> <configfiles> <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="alpha_diversity" type="data" format="qza" label="alpha_diversity: SampleData[AlphaDiversity]" help="[required] Vector of alpha diversity values by sample."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="SampleData[AlphaDiversity]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[AlphaDiversity]']</validator> </param> <repeat name="metadata" min="1" help="[required] The sample metadata." title="metadata: Metadata"> <conditional name="__q2galaxy__GUI__conditional__metadata__"> <param name="type" type="select" label="metadata: Metadata"> <option value="tsv" selected="true">Metadata from TSV</option> <option value="qza">Metadata from Artifact</option> </param> <when value="tsv"> <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> </when> <when value="qza"> <param name="source" type="data" format="qza" label="Metadata Source"/> </when> </conditional> </repeat> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> <param name="method" type="select" label="method: Str % Choices('spearman', 'pearson')" display="radio"> <option value="spearman" selected="true">spearman</option> <option value="pearson">pearson</option> </param> <param name="intersect_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="intersect_ids: Bool" help="[default: No] If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs."/> </section> </inputs> <outputs> <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> </outputs> <tests> <test> <param name="alpha_diversity" value="alpha_correlation.test0.alpha-div-faith-pd.qza" ftype="qza"/> <repeat name="metadata"> <conditional name="__q2galaxy__GUI__conditional__metadata__"> <param name="type" value="tsv"/> <param name="source" value="alpha_correlation.test0.metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> <output name="visualization" ftype="qzv"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> <has_line_matching expression="type: Visualization"/> </has_archive_member> </assert_contents> </output> </test> </tests> <help> QIIME 2: diversity alpha-correlation ==================================== Alpha diversity correlation Outputs: -------- :visualization.qzv: <no description> | Description: ------------ Determine whether numeric sample metadata columns are correlated with alpha diversity. Examples: --------- alpha_correlation_faith_pd ************************** Using the ``qiime2 diversity alpha-correlation`` tool: #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza`` #. For *"metadata"*: - Perform the following steps. #. Leave as ``Metadata from TSV`` #. Set *"Metadata Source"* to ``metadata.tsv`` #. Press the ``Execute`` button. | </help> <citations> <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>