Mercurial > repos > q2d2 > qiime2__diversity_lib__bray_curtis
changeset 3:6e6d848f2b5b draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
line wrap: on
line diff
--- a/qiime2__diversity_lib__bray_curtis.xml Thu Jun 08 19:38:27 2023 +0000 +++ b/qiime2__diversity_lib__bray_curtis.xml Thu Apr 25 21:02:45 2024 +0000 @@ -1,46 +1,33 @@ <?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 bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 diversity-lib bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Bray-Curtis Dissimilarity</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 bray_curtis '$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 for which Bray-Curtis dissimilarity should be computed."> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required] The feature table containing the samples for which Bray-Curtis dissimilarity should be computed."> <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> <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> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator> </param> - <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> - <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> <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/> @@ -58,10 +45,6 @@ </test> <test> <param name="table" value="bray_curtis.test1.feature-table.qza" ftype="qza"/> - <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"> @@ -72,10 +55,6 @@ </test> <test> <param name="table" value="bray_curtis.test2.feature-table.qza" ftype="qza"/> - <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"> @@ -126,10 +105,6 @@ ************************************************************* Using the ``qiime2 diversity-lib bray-curtis`` tool: #. Set *"table"* to ``#: feature-table.qza`` - #. 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: @@ -148,10 +123,6 @@ ************************************************************* Using the ``qiime2 diversity-lib bray-curtis`` tool: #. Set *"table"* to ``#: feature-table.qza`` - #. 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: