| Next changeset 1:fe99db171ce5 (2023-06-08) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 69da7976573cc07a363ac66bdacc9269d7cd3732 |
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added:
qiime2__composition__ancombc.xml test-data/ancombc.test0.metadata.tsv test-data/ancombc.test0.table.qza test-data/ancombc.test1.metadata.tsv test-data/ancombc.test1.table.qza |
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| diff -r 000000000000 -r 9b2a68d3017f qiime2__composition__ancombc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__composition__ancombc.xml Fri Jan 13 22:04:42 2023 +0000 |
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| b'@@ -0,0 +1,209 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+<!--\n+Copyright (c) 2023, 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: 2022.11.1)\n+for:\n+ qiime2 (version: 2022.11.1)\n+-->\n+<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">\n+ <description>Analysis of Composition of Microbiomes with Bias Correction</description>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/core:2022.11</container>\n+ </requirements>\n+ <version_command>q2galaxy version composition</version_command>\n+ <command detect_errors="exit_code">q2galaxy run composition ancombc \'$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 to be used for ANCOM computation.">\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+ <repeat name="metadata" min="1" help="[required] The sample metadata." title="metadata: Metadata">\n+ <conditional name="__q2galaxy__GUI__conditional__metadata__">\n+ <param name="type" type="select" label="metadata: Metadata">\n+ <option value="tsv" selected="true">Metadata from TSV</option>\n+ <option value="qza">Metadata from Artifact</option>\n+ </param>\n+ <when value="tsv">\n+ <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>\n+ </when>\n+ <when value="qza">\n+ <param name="source" type="data" format="qza" label="Metadata Source"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ <param name="formula" type="text" label="formula: Str" help="[required] How the microbial absolute abundances for each taxon depend on the variables within the `metadata`.">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <param name="p_adj_method" type="select" label="p_adj_method: Str % Choices(\'holm\', \'hochberg\', \'hommel\', \'bonferroni\', \'BH\', \'BY\', \'fdr\', \'none\')">\n+ <option value="holm" selected="true">holm</option>\n+ <option value="hochberg">hochberg</option>\n+ <option value="hommel">hommel</option>\n+ <option value="bonferroni">bonferroni</option>\n+ <option value="BH">BH</option>\n+ <option value="BY">BY</option>\n+ <option value="fdr">fdr</option>\n+ <option value="none">none</option>\n+ </param>\n+ <param name="prv_cut" type="float" value="0.1" label="prv_cut: Float" help="[default: 0.1] A numerical fraction between 0-1. Taxa with prevalences less than this value will be excluded from the analysis."/>\n+ <param name="lib_cut" type="integer" value="0" label="lib_cut: Int" help="[default: 0] A numerical threshold for filtering samples based on library sizes. Samples with library sizes less than this value will be excluded from the analysis."/>\n+ <repeat name="r'..b'.metadata.tsv" ftype="qiime2.tabular"/>\n+ </conditional>\n+ </repeat>\n+ <param name="formula" value="bodysite"/>\n+ <output name="differentials" ftype="qza">\n+ <assert_contents>\n+ <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">\n+ <has_line_matching expression="type: FeatureData\\[DifferentialAbundance\\]"/>\n+ </has_archive_member>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="table" value="ancombc.test1.table.qza" ftype="qza"/>\n+ <repeat name="metadata">\n+ <conditional name="__q2galaxy__GUI__conditional__metadata__">\n+ <param name="type" value="tsv"/>\n+ <param name="source" value="ancombc.test1.metadata.tsv" ftype="qiime2.tabular"/>\n+ </conditional>\n+ </repeat>\n+ <param name="formula" value="bodysite + month"/>\n+ <repeat name="reference_levels">\n+ <param name="element" value="bodysite::tongue"/>\n+ </repeat>\n+ <output name="differentials" ftype="qza">\n+ <assert_contents>\n+ <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">\n+ <has_line_matching expression="type: FeatureData\\[DifferentialAbundance\\]"/>\n+ </has_archive_member>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+QIIME 2: composition ancombc\n+============================\n+Analysis of Composition of Microbiomes with Bias Correction\n+\n+\n+Outputs:\n+--------\n+:differentials.qza: The calculated per-feature differentials.\n+\n+| \n+\n+Description:\n+------------\n+ANCOM-BC description goes here.\n+\n+Examples:\n+---------\n+\n+ancombc_single_formula\n+**********************\n+Using the ``qiime2 composition ancombc`` tool:\n+ #. Set *"table"* to ``#: table.qza``\n+ #. For *"metadata"*:\n+\n+ - Perform the following steps.\n+\n+ #. Leave as ``Metadata from TSV``\n+ #. Set *"Metadata Source"* to ``metadata.tsv``\n+\n+\n+ #. Set *"formula"* to ``bodysite``\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 composition ancombc [...] : differentials.qza``\n+ - ``dataloaf.qza``\n+\n+ancombc_multi_formula_with_reference_levels\n+*******************************************\n+Using the ``qiime2 composition ancombc`` tool:\n+ #. Set *"table"* to ``#: table.qza``\n+ #. For *"metadata"*:\n+\n+ - Perform the following steps.\n+\n+ #. Leave as ``Metadata from TSV``\n+ #. Set *"Metadata Source"* to ``metadata.tsv``\n+\n+\n+ #. Set *"formula"* to ``bodysite + month``\n+ #. Expand the ``additional options`` section\n+\n+ - For *"reference_levels"*:\n+\n+ #. Set *"element"* to ``bodysite::tongue``\n+ #. (Do not insert additional values.)\n+\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 composition ancombc [...] : differentials.qza``\n+ - ``dataloaf.qza``\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="doi">10.3402/mehd.v26.27663</citation>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 9b2a68d3017f test-data/ancombc.test0.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ancombc.test0.metadata.tsv Fri Jan 13 22:04:42 2023 +0000 |
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| @@ -0,0 +1,36 @@ +sample-id barcode-sequence bodysite month day subject animal testcolumn singlecolumn AZcolumn +#q2:types categorical categorical numeric numeric categorical categorical categorical categorical categorical +L1S8 AGCTGACTAGTC gut 10 28 subject-1 dog test1 value A +L1S57 ACACACTATGGC gut 1 20 subject-1 dog test2 value Z +L1S76 ACTACGTGTGGT gut 2 17 subject-1 cow test1 value Z +L1S105 AGTGCGATGCGT gut 3 17 subject-1 cat test2 value A +L2S155 ACGATGCGACCA left palm 1 20 subject-1 cat test1 value A +L2S175 AGCTATCCACGA left palm 2 17 subject-1 cat test2 value A +L2S204 ATGCAGCTCAGT left palm 3 17 subject-1 bird test1 value Z +L2S222 CACGTGACATGT left palm 4 14 subject-1 cow test2 value Z +L3S242 ACAGTTGCGCGA right palm 10 28 subject-1 bird test1 value A +L3S294 CACGACAGGCTA right palm 1 20 subject-1 dog test2 value Z +L3S313 AGTGTCACGGTG right palm 2 17 subject-1 dog test1 value Z +L3S341 CAAGTGAGAGAG right palm 3 17 subject-1 cat test2 value Z +L3S360 CATCGTATCAAC right palm 4 14 subject-1 cat test1 value A +L5S104 CAGTGTCAGGAC tongue 10 28 subject-1 bird test2 value A +L5S155 ATCTTAGACTGC tongue 1 20 subject-1 cow test1 value Z +L5S174 CAGACATTGCGT tongue 2 17 subject-1 dog test2 value A +L5S203 CGATGCACCAGA tongue 3 17 subject-1 cat test1 value Z +L5S222 CTAGAGACTCTT tongue 4 14 subject-1 bird test2 value Z +L1S140 ATGGCAGCTCTA gut 10 28 subject-2 dog test1 value Z +L1S208 CTGAGATACGCG gut 1 20 subject-2 dog test2 value A +L1S257 CCGACTGAGATG gut 3 17 subject-2 dog test1 value A +L1S281 CCTCTCGTGATC gut 4 14 subject-2 cat test2 value Z +L2S240 CATATCGCAGTT left palm 10 28 subject-2 cat test1 value A +L2S309 CGTGCATTATCA left palm 1 20 subject-2 cat test2 value A +L2S357 CTAACGCAGTCA left palm 3 17 subject-2 bird test1 value Z +L2S382 CTCAATGACTCA left palm 4 14 subject-2 bird test2 value A +L3S378 ATCGATCTGTGG right palm 10 28 subject-2 cow test1 value Z +L4S63 CTCGTGGAGTAG right palm 1 20 subject-2 dog test2 value Z +L4S112 GCGTTACACACA right palm 3 17 subject-2 cat test1 value A +L4S137 GAACTGTATCTC right palm 4 14 subject-2 bird test2 value A +L5S240 CTGGACTCATAG tongue 10 28 subject-2 dog test1 value A +L6S93 GCGTTACACACA tongue 3 17 subject-2 dog test1 value Z +L6S20 GAACTGTATCTC tongue 4 14 subject-2 bird test2 value Z +L6S68 CTGGACTCATAG gut 10 28 subject-2 cow test1 value Z |
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| diff -r 000000000000 -r 9b2a68d3017f test-data/ancombc.test1.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ancombc.test1.metadata.tsv Fri Jan 13 22:04:42 2023 +0000 |
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| @@ -0,0 +1,36 @@ +sample-id barcode-sequence bodysite month day subject animal testcolumn singlecolumn AZcolumn +#q2:types categorical categorical numeric numeric categorical categorical categorical categorical categorical +L1S8 AGCTGACTAGTC gut 10 28 subject-1 dog test1 value A +L1S57 ACACACTATGGC gut 1 20 subject-1 dog test2 value Z +L1S76 ACTACGTGTGGT gut 2 17 subject-1 cow test1 value Z +L1S105 AGTGCGATGCGT gut 3 17 subject-1 cat test2 value A +L2S155 ACGATGCGACCA left palm 1 20 subject-1 cat test1 value A +L2S175 AGCTATCCACGA left palm 2 17 subject-1 cat test2 value A +L2S204 ATGCAGCTCAGT left palm 3 17 subject-1 bird test1 value Z +L2S222 CACGTGACATGT left palm 4 14 subject-1 cow test2 value Z +L3S242 ACAGTTGCGCGA right palm 10 28 subject-1 bird test1 value A +L3S294 CACGACAGGCTA right palm 1 20 subject-1 dog test2 value Z +L3S313 AGTGTCACGGTG right palm 2 17 subject-1 dog test1 value Z +L3S341 CAAGTGAGAGAG right palm 3 17 subject-1 cat test2 value Z +L3S360 CATCGTATCAAC right palm 4 14 subject-1 cat test1 value A +L5S104 CAGTGTCAGGAC tongue 10 28 subject-1 bird test2 value A +L5S155 ATCTTAGACTGC tongue 1 20 subject-1 cow test1 value Z +L5S174 CAGACATTGCGT tongue 2 17 subject-1 dog test2 value A +L5S203 CGATGCACCAGA tongue 3 17 subject-1 cat test1 value Z +L5S222 CTAGAGACTCTT tongue 4 14 subject-1 bird test2 value Z +L1S140 ATGGCAGCTCTA gut 10 28 subject-2 dog test1 value Z +L1S208 CTGAGATACGCG gut 1 20 subject-2 dog test2 value A +L1S257 CCGACTGAGATG gut 3 17 subject-2 dog test1 value A +L1S281 CCTCTCGTGATC gut 4 14 subject-2 cat test2 value Z +L2S240 CATATCGCAGTT left palm 10 28 subject-2 cat test1 value A +L2S309 CGTGCATTATCA left palm 1 20 subject-2 cat test2 value A +L2S357 CTAACGCAGTCA left palm 3 17 subject-2 bird test1 value Z +L2S382 CTCAATGACTCA left palm 4 14 subject-2 bird test2 value A +L3S378 ATCGATCTGTGG right palm 10 28 subject-2 cow test1 value Z +L4S63 CTCGTGGAGTAG right palm 1 20 subject-2 dog test2 value Z +L4S112 GCGTTACACACA right palm 3 17 subject-2 cat test1 value A +L4S137 GAACTGTATCTC right palm 4 14 subject-2 bird test2 value A +L5S240 CTGGACTCATAG tongue 10 28 subject-2 dog test1 value A +L6S93 GCGTTACACACA tongue 3 17 subject-2 dog test1 value Z +L6S20 GAACTGTATCTC tongue 4 14 subject-2 bird test2 value Z +L6S68 CTGGACTCATAG gut 10 28 subject-2 cow test1 value Z |
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