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author | q2d2 |
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date | Mon, 03 Jun 2024 23:18:33 +0000 |
parents | f7e81c151e17 |
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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-correlation" id="qiime2__diversity__beta_correlation" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> <description>Beta diversity correlation</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_correlation '$inputs'</command> <configfiles> <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="distance_matrix" type="data" format="qza" label="distance_matrix: 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> <conditional name="metadata"> <param name="type" type="select" label="metadata: MetadataColumn[Numeric]" help="[required] Numeric metadata column from which to compute pairwise Euclidean distances"> <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"/> <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> </param> </when> <when value="qza"> <param name="source" type="data" format="qza" label="Metadata Source"/> <param name="column" type="text" label="Column Name"> <validator type="empty_field"/> </param> </when> </conditional> <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" label="label1: Str" help="[default: 'Distance Matrix'] Label for `distance_matrix` in the output visualization."> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> <param name="label2" type="text" value="Metadata" label="label2: Str" help="[default: 'Metadata'] Label for `metadata_distance_matrix` in the output visualization."> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> </section> </inputs> <outputs> <data name="metadata_distance_matrix" format="qza" label="${tool.name} on ${on_string}: metadata_distance_matrix.qza" from_work_dir="metadata_distance_matrix.qza"/> <data name="mantel_scatter_visualization" format="qzv" label="${tool.name} on ${on_string}: mantel_scatter_visualization.qzv" from_work_dir="mantel_scatter_visualization.qzv"/> </outputs> <tests/> <help> QIIME 2: diversity beta-correlation =================================== Beta diversity correlation Outputs: -------- :metadata_distance_matrix.qza: The Distance Matrix produced from the metadata column and used in the mantel test :mantel_scatter_visualization.qzv: Scatter plot rendering of the manteltest results | Description: ------------ Create a distance matrix from a numeric metadata column and apply a two-sided Mantel test to identify correlation between two distance matrices. Actions used internally: `distance-matrix` from q2-metadata and `mantel` from q2-diversity. | </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>