| Next changeset 1:66045b02d6c1 (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_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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added:
qiime2__diversity_lib__beta_passthrough.xml test-data/alpha_passthrough.test0.feature-table.qza test-data/beta_passthrough.test0.feature-table.qza test-data/beta_passthrough.test1.feature-table.qza test-data/beta_passthrough.test2.feature-table.qza test-data/beta_passthrough.test3.feature-table.qza test-data/beta_phylogenetic_meta_passthrough.test0.feature-table1.qza test-data/beta_phylogenetic_meta_passthrough.test0.feature-table2.qza test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny1.qza test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny2.qza test-data/beta_phylogenetic_meta_passthrough.test1.feature-table1.qza test-data/beta_phylogenetic_meta_passthrough.test1.feature-table2.qza test-data/beta_phylogenetic_meta_passthrough.test1.phylogeny.qza test-data/beta_phylogenetic_meta_passthrough.test2.feature-table1.qza test-data/beta_phylogenetic_meta_passthrough.test2.feature-table2.qza test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny1.qza test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny2.qza test-data/beta_phylogenetic_passthrough.test0.feature-table.qza test-data/beta_phylogenetic_passthrough.test0.phylogeny.qza test-data/beta_phylogenetic_passthrough.test1.feature-table.qza test-data/beta_phylogenetic_passthrough.test1.phylogeny.qza test-data/beta_phylogenetic_passthrough.test2.feature-table.qza test-data/beta_phylogenetic_passthrough.test2.phylogeny.qza test-data/beta_phylogenetic_passthrough.test3.feature-table.qza test-data/beta_phylogenetic_passthrough.test3.phylogeny.qza test-data/beta_phylogenetic_passthrough.test4.feature-table.qza test-data/beta_phylogenetic_passthrough.test4.phylogeny.qza test-data/beta_phylogenetic_passthrough.test5.feature-table.qza test-data/beta_phylogenetic_passthrough.test5.phylogeny.qza test-data/beta_phylogenetic_passthrough.test6.feature-table.qza test-data/beta_phylogenetic_passthrough.test6.phylogeny.qza test-data/bray_curtis.test0.feature-table.qza test-data/bray_curtis.test1.feature-table.qza test-data/bray_curtis.test2.feature-table.qza test-data/faith_pd.test0.feature-table.qza test-data/faith_pd.test0.phylogeny.qza test-data/jaccard.test0.feature-table.qza test-data/jaccard.test1.feature-table.qza test-data/jaccard.test2.feature-table.qza test-data/observed_features.test0.feature-table.qza test-data/pielou_evenness.test0.feature-table.qza test-data/pielou_evenness.test1.feature-table.qza test-data/shannon_entropy.test0.feature-table.qza test-data/shannon_entropy.test1.feature-table.qza test-data/unweighted_unifrac.test0.feature-table.qza test-data/unweighted_unifrac.test0.phylogeny.qza test-data/unweighted_unifrac.test1.feature-table.qza test-data/unweighted_unifrac.test1.phylogeny.qza test-data/unweighted_unifrac.test2.feature-table.qza test-data/unweighted_unifrac.test2.phylogeny.qza test-data/unweighted_unifrac.test3.feature-table.qza test-data/unweighted_unifrac.test3.phylogeny.qza test-data/weighted_unifrac.test0.feature-table.qza test-data/weighted_unifrac.test0.phylogeny.qza test-data/weighted_unifrac.test1.feature-table.qza test-data/weighted_unifrac.test1.phylogeny.qza test-data/weighted_unifrac.test2.feature-table.qza test-data/weighted_unifrac.test2.phylogeny.qza test-data/weighted_unifrac.test3.feature-table.qza test-data/weighted_unifrac.test3.phylogeny.qza |
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| diff -r 000000000000 -r da97d578001c qiime2__diversity_lib__beta_passthrough.xml --- /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 |
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| b'@@ -0,0 +1,249 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+<!--\n+Copyright (c) 2022, QIIME 2 development team.\n+\n+Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)\n+-->\n+<!--\n+This tool was automatically generated by:\n+ q2galaxy (version: 2022.8.1)\n+for:\n+ qiime2 (version: 2022.8.1)\n+-->\n+<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">\n+ <description>Beta Passthrough (non-phylogenetic)</description>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/core:2022.8</container>\n+ </requirements>\n+ <version_command>q2galaxy version diversity_lib</version_command>\n+ <command detect_errors="aggressive">q2galaxy run diversity_lib beta_passthrough \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="paths"/>\n+ </configfiles>\n+ <inputs>\n+ <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.">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="FeatureTable[Frequency]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'FeatureTable[Frequency]\']</validator>\n+ </param>\n+ <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\')">\n+ <option value="__q2galaxy__::literal::None">Selection required</option>\n+ <option value="aitchison">aitchison</option>\n+ <option value="canberra">canberra</option>\n+ <option value="canberra_adkins">canberra_adkins</option>\n+ <option value="chebyshev">chebyshev</option>\n+ <option value="cityblock">cityblock</option>\n+ <option value="correlation">correlation</option>\n+ <option value="cosine">cosine</option>\n+ <option value="dice">dice</option>\n+ <option value="euclidean">euclidean</option>\n+ <option value="hamming">hamming</option>\n+ <option value="jensenshannon">jensenshannon</option>\n+ <option value="kulsinski">kulsinski</option>\n+ <option value="matching">matching</option>\n+ <option value="minkowski">minkowski</option>\n+ <option value="rogerstanimoto">rogerstanimoto</option>\n+ <option value="russellrao">russellrao</option>\n+ <option value="seuclidean">seuclidean</option>\n+ <option value="sokalmichener">sokalmichener</option>\n+ <option value="sokalsneath">sokalsneath</option>\n+ <option value="sqeuclidean">sqeuclidean</option>\n+ <option value="yule">yule</option>\n+ <validator type="expression" message="Please verify this parameter.">value != \'__q2galaxy__::literal::None\'</validator>\n+ </param>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <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."/>\n+ <conditional name="__q2galaxy__GUI__conditional__n_jobs__">\n+ <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 thi'..b'>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+QIIME 2: diversity-lib beta-passthrough\n+=======================================\n+Beta Passthrough (non-phylogenetic)\n+\n+\n+Outputs:\n+--------\n+:distance_matrix.qza: The resulting distance matrix.\n+\n+| \n+\n+Description:\n+------------\n+Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.\n+\n+Examples:\n+---------\n+\n+run on one core (by default)\n+****************************\n+Using the ``qiime2 diversity-lib beta-passthrough`` tool:\n+ #. Set *"table"* to ``#: feature-table.qza``\n+ #. Set *"metric"* to ``euclidean``\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza``\n+ - ``euclidean-dm.qza``\n+\n+to run on n cores, replace 1 here with your preferred integer\n+*************************************************************\n+Using the ``qiime2 diversity-lib beta-passthrough`` tool:\n+ #. Set *"table"* to ``#: feature-table.qza``\n+ #. Set *"metric"* to ``kulsinski``\n+ #. Expand the ``additional options`` section\n+\n+ - Leave *"n_jobs"* as its default value of ``1``\n+\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza``\n+ - ``kulsinski-dm.qza``\n+\n+use \'auto\' to run on all of host system\'s available CPU cores\n+*************************************************************\n+| A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.\n+Using the ``qiime2 diversity-lib beta-passthrough`` tool:\n+ #. Set *"table"* to ``#: feature-table.qza``\n+ #. Set *"metric"* to ``aitchison``\n+ #. Expand the ``additional options`` section\n+\n+ - Set *"n_jobs"* to ``auto``\n+\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza``\n+ - ``aitchison-dm.qza``\n+\n+use \'pseudocount\' to manually set a pseudocount for compositional metrics\n+*************************************************************************\n+Using the ``qiime2 diversity-lib beta-passthrough`` tool:\n+ #. Set *"table"* to ``#: feature-table.qza``\n+ #. Set *"metric"* to ``aitchison``\n+ #. Expand the ``additional options`` section\n+\n+ #. Set *"pseudocount"* to ``5``\n+ #. Set *"n_jobs"* to ``auto``\n+\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza``\n+ - ``aitchison-dm.qza``\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n' |
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