| Previous changeset 4:cb1a60431256 (2024-10-30) Next changeset 6:c0c74c592ff7 (2025-07-15) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit b1fccfb38b4873cd4699743033449014a2978e7d |
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modified:
qiime2__composition__tabulate.xml test-data/ancombc.test0.table.qza test-data/ancombc.test1.table.qza |
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added:
test-data/ancombc2.test0.metadata.tsv test-data/ancombc2.test0.table.qza test-data/ancombc2.test1.metadata.tsv test-data/ancombc2.test1.table.qza |
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| diff -r cb1a60431256 -r 600f11a2839d qiime2__composition__tabulate.xml --- a/qiime2__composition__tabulate.xml Wed Oct 30 19:36:12 2024 +0000 +++ b/qiime2__composition__tabulate.xml Mon May 05 18:41:25 2025 +0000 |
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| @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2024, QIIME 2 development team. +Copyright (c) 2025, 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: 2024.10.0) + q2galaxy (version: 2025.4.0) for: - qiime2 (version: 2024.10.1) + qiime2 (version: 2025.4.0) --> -<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> - <description> View tabular output from ANCOM-BC.</description> +<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause"> + <description> View tabular output from ANCOM-BC or ANCOM-BC2.</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2024.10</container> + <container type="docker">quay.io/qiime2/amplicon:2025.4</container> </requirements> <version_command>q2galaxy version composition</version_command> <command detect_errors="exit_code">q2galaxy run composition tabulate '$inputs'</command> @@ -24,11 +24,12 @@ <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> - <param name="data" type="data" format="qza" label="data: FeatureData[DifferentialAbundance]" help="[required] The ANCOM-BC output to be tabulated."> + <param name="data" type="data" format="qza" label="data: FeatureData[DifferentialAbundance | ANCOMBC2Output]" help="[required] The ANCOM-BC or ANCOM-BC2 output to be tabulated."> <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[ANCOMBC2Output]"/> <filter type="add_value" value="FeatureData[DifferentialAbundance]"/> </options> - <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DifferentialAbundance]']</validator> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[ANCOMBC2Output]', 'FeatureData[DifferentialAbundance]']</validator> </param> </inputs> <outputs> @@ -38,7 +39,7 @@ <help> QIIME 2: composition tabulate ============================= - View tabular output from ANCOM-BC. + View tabular output from ANCOM-BC or ANCOM-BC2. Outputs: @@ -49,7 +50,7 @@ Description: ------------ -Generate tabular view of ANCOM-BC output, which includes per-page views for the log-fold change (lfc), standard error (se), P values, Q values, and W scores. +Generate tabular view of ANCOM-BC or ANCOM-BC2 output, which includes per-page views for the log-fold change (lfc), standard error (se), P values, Q values, and W scores. | |
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| diff -r cb1a60431256 -r 600f11a2839d test-data/ancombc2.test0.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ancombc2.test0.metadata.tsv Mon May 05 18:41:25 2025 +0000 |
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| @@ -0,0 +1,39 @@ +sample-id barcode-sequence bodysite month day subject animal testcolumn singlecolumn AZcolumn +#q2:types categorical categorical categorical 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 +L6SD93 GCGTTACACACA toe 3 17 subject-2 dog test1 value +L6SD20 GAACTGTATCTC toe 4 14 subject-2 bird test2 value +L6SD68 CTGGACTCATAG toe 10 28 subject-2 cow test1 value |
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| diff -r cb1a60431256 -r 600f11a2839d test-data/ancombc2.test1.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ancombc2.test1.metadata.tsv Mon May 05 18:41:25 2025 +0000 |
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| @@ -0,0 +1,39 @@ +sample-id barcode-sequence bodysite month day subject animal testcolumn singlecolumn AZcolumn +#q2:types categorical categorical categorical 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 +L6SD93 GCGTTACACACA toe 3 17 subject-2 dog test1 value +L6SD20 GAACTGTATCTC toe 4 14 subject-2 bird test2 value +L6SD68 CTGGACTCATAG toe 10 28 subject-2 cow test1 value |
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