Mercurial > repos > q2d2 > qiime2__diversity_lib__beta_passthrough
changeset 3:0969c54eddc6 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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--- a/qiime2__diversity_lib__beta_passthrough.xml Thu Jun 08 19:41:21 2023 +0000 +++ b/qiime2__diversity_lib__beta_passthrough.xml Thu Apr 25 21:03:38 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-lib beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 diversity-lib beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Beta Passthrough (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_lib</version_command> <command detect_errors="exit_code">q2galaxy run diversity_lib beta_passthrough '$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 beta diversity should be computed."> @@ -54,18 +54,6 @@ </param> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> <param name="pseudocount" type="integer" min="1" value="1" label="pseudocount: Int % Range(1, None)" help="[default: 1] A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics."/> - <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] 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] 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> @@ -86,10 +74,6 @@ <test> <param name="table" value="beta_passthrough.test1.feature-table.qza" ftype="qza"/> <param name="metric" value="kulsinski"/> - <conditional name="__q2galaxy__GUI__conditional__n_jobs__"> - <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/> - <param name="n_jobs" value="1"/> - </conditional> <output name="distance_matrix" ftype="qza"> <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"> @@ -101,10 +85,6 @@ <test> <param name="table" value="beta_passthrough.test2.feature-table.qza" ftype="qza"/> <param name="metric" value="aitchison"/> - <conditional name="__q2galaxy__GUI__conditional__n_jobs__"> - <param name="__q2galaxy__GUI__select__" value="auto"/> - <param name="n_jobs" value="auto"/> - </conditional> <output name="distance_matrix" ftype="qza"> <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"> @@ -117,10 +97,6 @@ <param name="table" value="beta_passthrough.test3.feature-table.qza" ftype="qza"/> <param name="metric" value="aitchison"/> <param name="pseudocount" value="5"/> - <conditional name="__q2galaxy__GUI__conditional__n_jobs__"> - <param name="__q2galaxy__GUI__select__" value="auto"/> - <param name="n_jobs" value="auto"/> - </conditional> <output name="distance_matrix" ftype="qza"> <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"> @@ -173,10 +149,6 @@ Using the ``qiime2 diversity-lib beta-passthrough`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Set *"metric"* to ``kulsinski`` - #. Expand the ``additional options`` section - - - Leave *"n_jobs"* as its default value of ``1`` - #. Press the ``Execute`` button. Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: @@ -197,10 +169,6 @@ Using the ``qiime2 diversity-lib beta-passthrough`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Set *"metric"* to ``aitchison`` - #. Expand the ``additional options`` section - - - Set *"n_jobs"* to ``auto`` - #. Press the ``Execute`` button. Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: @@ -222,8 +190,7 @@ #. Set *"metric"* to ``aitchison`` #. Expand the ``additional options`` section - #. Set *"pseudocount"* to ``5`` - #. Set *"n_jobs"* to ``auto`` + - Set *"pseudocount"* to ``5`` #. Press the ``Execute`` button.