Mercurial > repos > q2d2 > qiime2__diversity__core_metrics_phylogenetic
changeset 3:76e136962089 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 20:57:05 +0000 |
| parents | 9d29f6a334e5 |
| children | d14296c8a1b8 |
| files | qiime2__diversity__core_metrics_phylogenetic.xml test-data/alpha_correlation.test0.alpha-div-faith-pd.qza test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza |
| diffstat | 3 files changed, 7 insertions(+), 18 deletions(-) [+] |
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--- a/qiime2__diversity__core_metrics_phylogenetic.xml Thu Jun 08 19:37:36 2023 +0000 +++ b/qiime2__diversity__core_metrics_phylogenetic.xml Thu Apr 25 20:57:05 2024 +0000 @@ -1,24 +1,24 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2023, QIIME 2 development team. +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: 2023.5.0) + q2galaxy (version: 2024.2.1) for: - qiime2 (version: 2023.5.1) + qiime2 (version: 2024.2.0) --> -<tool name="qiime2 diversity core-metrics-phylogenetic" id="qiime2__diversity__core_metrics_phylogenetic" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 diversity core-metrics-phylogenetic" id="qiime2__diversity__core_metrics_phylogenetic" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Core diversity metrics (phylogenetic and non-phylogenetic)</description> <requirements> - <container type="docker">quay.io/qiime2/core:2023.5</container> + <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 core_metrics_phylogenetic '$inputs'</command> <configfiles> - <inputs name="inputs" data_style="paths"/> + <inputs name="inputs" data_style="staging_path_and_source_path"/> </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."> @@ -50,18 +50,7 @@ </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_or_threads__"> - <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs_or_threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] [beta/beta-phylogenetic methods only] - The number of concurrent jobs or CPU threads to use in performing this calculation. Individual methods will create jobs/threads as implemented in q2-diversity-lib dependencies. May not exceed the number of available physical cores. If n_jobs_or_threads = 'auto', one thread/job will be created 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_or_threads" type="hidden" value="auto"/> - </when> - <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> - <param name="n_jobs_or_threads" type="integer" min="1" value="1" label="n_jobs_or_threads: Int % Range(1, None)" help="[default: 1] [beta/beta-phylogenetic methods only] - The number of concurrent jobs or CPU threads to use in performing this calculation. Individual methods will create jobs/threads as implemented in q2-diversity-lib dependencies. May not exceed the number of available physical cores. If n_jobs_or_threads = 'auto', one thread/job will be created for each identified CPU core on the host."/> - </when> - </conditional> + <param name="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No] If set to `True` samples and features without metadata are included by setting all metadata values to: "This element has no metadata". By default an exception will be raised if missing elements are encountered. Note, this flag only takes effect if there is at least one overlapping element."/> </section> </inputs> <outputs>