Mercurial > repos > q2d2 > qiime2__diversity_lib__beta_passthrough
changeset 0:da97d578001c draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__diversity_lib__beta_passthrough.xml Mon Aug 29 19:45:35 2022 +0000 @@ -0,0 +1,249 @@ +<?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-lib beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Beta Passthrough (non-phylogenetic)</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version diversity_lib</version_command> + <command detect_errors="aggressive">q2galaxy run diversity_lib beta_passthrough '$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 beta diversity 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="metric" type="select" label="metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'kulsinski', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="aitchison">aitchison</option> + <option value="canberra">canberra</option> + <option value="canberra_adkins">canberra_adkins</option> + <option value="chebyshev">chebyshev</option> + <option value="cityblock">cityblock</option> + <option value="correlation">correlation</option> + <option value="cosine">cosine</option> + <option value="dice">dice</option> + <option value="euclidean">euclidean</option> + <option value="hamming">hamming</option> + <option value="jensenshannon">jensenshannon</option> + <option value="kulsinski">kulsinski</option> + <option value="matching">matching</option> + <option value="minkowski">minkowski</option> + <option value="rogerstanimoto">rogerstanimoto</option> + <option value="russellrao">russellrao</option> + <option value="seuclidean">seuclidean</option> + <option value="sokalmichener">sokalmichener</option> + <option value="sokalsneath">sokalsneath</option> + <option value="sqeuclidean">sqeuclidean</option> + <option value="yule">yule</option> + <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> + </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> + <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/> + </outputs> + <tests> + <test> + <param name="table" value="beta_passthrough.test0.feature-table.qza" ftype="qza"/> + <param name="metric" value="euclidean"/> + <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"> + <has_line_matching expression="type: DistanceMatrix"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <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"> + <has_line_matching expression="type: DistanceMatrix"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <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"> + <has_line_matching expression="type: DistanceMatrix"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <test> + <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"> + <has_line_matching expression="type: DistanceMatrix"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> + <help> +QIIME 2: diversity-lib beta-passthrough +======================================= +Beta Passthrough (non-phylogenetic) + + +Outputs: +-------- +:distance_matrix.qza: The resulting distance matrix. + +| + +Description: +------------ +Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric. + +Examples: +--------- + +run on one core (by default) +**************************** +Using the ``qiime2 diversity-lib beta-passthrough`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Set *"metric"* to ``euclidean`` + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`` + - ``euclidean-dm.qza`` + +to run on n cores, replace 1 here with your preferred integer +************************************************************* +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: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`` + - ``kulsinski-dm.qza`` + +use 'auto' to run on all of host system's available CPU cores +************************************************************* +| A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics. +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: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`` + - ``aitchison-dm.qza`` + +use 'pseudocount' to manually set a pseudocount for compositional metrics +************************************************************************* +Using the ``qiime2 diversity-lib beta-passthrough`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Set *"metric"* to ``aitchison`` + #. Expand the ``additional options`` section + + #. Set *"pseudocount"* to ``5`` + #. 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: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`` + - ``aitchison-dm.qza`` + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>