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author | q2d2 |
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date | Thu, 08 Jun 2023 19:37:05 +0000 |
parents | 4b8cdacb02f5 |
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<?xml version='1.0' encoding='utf-8'?> <!-- Copyright (c) 2023, 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: 2023.5.0) for: qiime2 (version: 2023.5.1) --> <tool name="qiime2 diversity core-metrics" id="qiime2__diversity__core_metrics" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> <description>Core diversity metrics (non-phylogenetic)</description> <requirements> <container type="docker">quay.io/qiime2/core:2023.5</container> </requirements> <version_command>q2galaxy version diversity</version_command> <command detect_errors="exit_code">q2galaxy run diversity core_metrics '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> <inputs> <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table containing the samples over which diversity metrics should be computed."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureTable[Frequency]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> </param> <param name="sampling_depth" type="integer" min="1" value="" label="sampling_depth: Int % Range(1, None)" help="[required] The total frequency that each sample should be rarefied to prior to computing diversity metrics."/> <repeat name="metadata" min="1" help="[required] The sample metadata to use in the emperor plots." 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="with_replacement" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="with_replacement: Bool" help="[default: No] Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement."/> <conditional name="__q2galaxy__GUI__conditional__n_jobs__"> <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] [beta methods only] - The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host."> <option value="auto">auto (Str)</option> <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option> </param> <when value="auto"> <param name="n_jobs" type="hidden" value="auto"/> </when> <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1] [beta methods only] - The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host."/> </when> </conditional> </section> </inputs> <outputs> <data name="rarefied_table" format="qza" label="${tool.name} on ${on_string}: rarefied_table.qza" from_work_dir="rarefied_table.qza"/> <data name="observed_features_vector" format="qza" label="${tool.name} on ${on_string}: observed_features_vector.qza" from_work_dir="observed_features_vector.qza"/> <data name="shannon_vector" format="qza" label="${tool.name} on ${on_string}: shannon_vector.qza" from_work_dir="shannon_vector.qza"/> <data name="evenness_vector" format="qza" label="${tool.name} on ${on_string}: evenness_vector.qza" from_work_dir="evenness_vector.qza"/> <data name="jaccard_distance_matrix" format="qza" label="${tool.name} on ${on_string}: jaccard_distance_matrix.qza" from_work_dir="jaccard_distance_matrix.qza"/> <data name="bray_curtis_distance_matrix" format="qza" label="${tool.name} on ${on_string}: bray_curtis_distance_matrix.qza" from_work_dir="bray_curtis_distance_matrix.qza"/> <data name="jaccard_pcoa_results" format="qza" label="${tool.name} on ${on_string}: jaccard_pcoa_results.qza" from_work_dir="jaccard_pcoa_results.qza"/> <data name="bray_curtis_pcoa_results" format="qza" label="${tool.name} on ${on_string}: bray_curtis_pcoa_results.qza" from_work_dir="bray_curtis_pcoa_results.qza"/> <data name="jaccard_emperor" format="qzv" label="${tool.name} on ${on_string}: jaccard_emperor.qzv" from_work_dir="jaccard_emperor.qzv"/> <data name="bray_curtis_emperor" format="qzv" label="${tool.name} on ${on_string}: bray_curtis_emperor.qzv" from_work_dir="bray_curtis_emperor.qzv"/> </outputs> <tests/> <help> QIIME 2: diversity core-metrics =============================== Core diversity metrics (non-phylogenetic) Outputs: -------- :rarefied_table.qza: The resulting rarefied feature table. :observed_features_vector.qza: Vector of Observed Features values by sample. :shannon_vector.qza: Vector of Shannon diversity values by sample. :evenness_vector.qza: Vector of Pielou's evenness values by sample. :jaccard_distance_matrix.qza: Matrix of Jaccard distances between pairs of samples. :bray_curtis_distance_matrix.qza: Matrix of Bray-Curtis distances between pairs of samples. :jaccard_pcoa_results.qza: PCoA matrix computed from Jaccard distances between samples. :bray_curtis_pcoa_results.qza: PCoA matrix computed from Bray-Curtis distances between samples. :jaccard_emperor.qzv: Emperor plot of the PCoA matrix computed from Jaccard. :bray_curtis_emperor.qzv: Emperor plot of the PCoA matrix computed from Bray-Curtis. | Description: ------------ Applies a collection of diversity metrics (non-phylogenetic) to a feature table. | </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>