# HG changeset patch # User q2d2 # Date 1746470461 0 # Node ID 0cbcee1e1f194c0de855970af4dfa7f7d3ff3d18 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit b1fccfb38b4873cd4699743033449014a2978e7d diff -r 000000000000 -r 0cbcee1e1f19 qiime2__composition__ancombc2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__composition__ancombc2.xml Mon May 05 18:41:01 2025 +0000 @@ -0,0 +1,239 @@ + + + + + ANCOM-BC2: Analysis of Composition of Microbiomes with Bias Correction 2. + + qiime2 + + + quay.io/qiime2/amplicon:2025.4 + + q2galaxy version composition + q2galaxy run composition ancombc2 '$inputs' + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]'] + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + +

+ + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +QIIME 2: composition ancombc2 +============================= +ANCOM-BC2: Analysis of Composition of Microbiomes with Bias Correction 2. + + +Outputs: +-------- +:ancombc2_output.qza: The estimated log fold changes and their standard errors for the variables included in the mixed effects model. Also includes the structural zero designations if the `structural_zeros` parameter is passed. + +| + +Description: +------------ +Calls the `ancombc2` function of the ANCOMBC software package. See the ANCOM-BC2 publication and source code for details. + +Examples: +--------- + +single-variable +*************** +Using the ``qiime2 composition ancombc2`` tool: + #. Set *"table"* to ``#: table.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"fixed_effects_formula"* to ``bodysite`` + #. 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 composition ancombc2 [...] : ancombc2_output.qza`` + - ``abc2-output.qza`` + +multi-variable-reference +************************ +Using the ``qiime2 composition ancombc2`` tool: + #. Set *"table"* to ``#: table.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"fixed_effects_formula"* to ``bodysite + animal`` + #. Expand the ``additional options`` section + + - For *"reference_levels"*, use the ``+ reference_levels`` button to add the corresponding values: + + #. Add *"element"* set to ``bodysite::tongue`` + #. Add *"element"* set to ``animal::dog`` + + + #. 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 composition ancombc2 [...] : ancombc2_output.qza`` + - ``abc2-output.qza`` + + +| + + + + https://www.nature.com/articles/s41592-023-02092-7 + 10.1038/s41587-019-0209-9 + + diff -r 000000000000 -r 0cbcee1e1f19 test-data/ancombc.test0.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ancombc.test0.metadata.tsv Mon May 05 18:41:01 2025 +0000 @@ -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 diff -r 000000000000 -r 0cbcee1e1f19 test-data/ancombc.test0.table.qza Binary file test-data/ancombc.test0.table.qza has changed diff -r 000000000000 -r 0cbcee1e1f19 test-data/ancombc.test1.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ancombc.test1.metadata.tsv Mon May 05 18:41:01 2025 +0000 @@ -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 diff -r 000000000000 -r 0cbcee1e1f19 test-data/ancombc.test1.table.qza Binary file test-data/ancombc.test1.table.qza has changed diff -r 000000000000 -r 0cbcee1e1f19 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 18:41:01 2025 +0000 @@ -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 diff -r 000000000000 -r 0cbcee1e1f19 test-data/ancombc2.test0.table.qza Binary file test-data/ancombc2.test0.table.qza has changed diff -r 000000000000 -r 0cbcee1e1f19 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 18:41:01 2025 +0000 @@ -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 diff -r 000000000000 -r 0cbcee1e1f19 test-data/ancombc2.test1.table.qza Binary file test-data/ancombc2.test1.table.qza has changed