| Next changeset 1:4b8cdacb02f5 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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added:
qiime2__diversity__core_metrics.xml test-data/.gitkeep |
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| diff -r 000000000000 -r c841290b1a15 qiime2__diversity__core_metrics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__diversity__core_metrics.xml Mon Aug 29 19:35:49 2022 +0000 |
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| @@ -0,0 +1,106 @@ +<?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 diversity core-metrics" id="qiime2__diversity__core_metrics" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Core diversity metrics (non-phylogenetic)</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version diversity</version_command> + <command detect_errors="aggressive">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> |