# HG changeset patch # User q2d2 # Date 1686252856 0 # Node ID fe99db171ce523bd9c07d56345a789b85d18eceb # Parent 9b2a68d3017fad97ede1a7a76b13311a2be453ee planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 65e4952f33eb335528e8553150e9097e5ea8f556 diff -r 9b2a68d3017f -r fe99db171ce5 qiime2__composition__ancombc.xml --- a/qiime2__composition__ancombc.xml Fri Jan 13 22:04:42 2023 +0000 +++ b/qiime2__composition__ancombc.xml Thu Jun 08 19:34:16 2023 +0000 @@ -6,14 +6,14 @@ --> - + Analysis of Composition of Microbiomes with Bias Correction - quay.io/qiime2/core:2022.11 + quay.io/qiime2/core:2023.5 q2galaxy version composition q2galaxy run composition ancombc '$inputs' @@ -21,7 +21,7 @@ - + @@ -104,10 +104,13 @@ - + + + + @@ -131,7 +134,7 @@ Description: ------------ -ANCOM-BC description goes here. +Apply Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) to identify features that are differentially abundant across groups. Examples: --------- @@ -175,13 +178,13 @@ #. Set *"Metadata Source"* to ``metadata.tsv`` - #. Set *"formula"* to ``bodysite + month`` + #. Set *"formula"* to ``bodysite + animal`` #. Expand the ``additional options`` section - - For *"reference_levels"*: + - For *"reference_levels"*, use the ``+ reference_levels`` button to add the corresponding values: - #. Set *"element"* to ``bodysite::tongue`` - #. (Do not insert additional values.) + #. Add *"element"* set to ``bodysite::tongue`` + #. Add *"element"* set to ``animal::dog`` #. Press the ``Execute`` button. @@ -203,7 +206,7 @@ - 10.3402/mehd.v26.27663 + 10.1038/s41467-020-17041-7 10.1038/s41587-019-0209-9 diff -r 9b2a68d3017f -r fe99db171ce5 test-data/ancombc.test0.metadata.tsv --- a/test-data/ancombc.test0.metadata.tsv Fri Jan 13 22:04:42 2023 +0000 +++ b/test-data/ancombc.test0.metadata.tsv Thu Jun 08 19:34:16 2023 +0000 @@ -1,5 +1,5 @@ sample-id barcode-sequence bodysite month day subject animal testcolumn singlecolumn AZcolumn -#q2:types categorical categorical numeric numeric categorical categorical categorical categorical categorical +#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 @@ -34,3 +34,6 @@ 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 9b2a68d3017f -r fe99db171ce5 test-data/ancombc.test0.table.qza Binary file test-data/ancombc.test0.table.qza has changed diff -r 9b2a68d3017f -r fe99db171ce5 test-data/ancombc.test1.metadata.tsv --- a/test-data/ancombc.test1.metadata.tsv Fri Jan 13 22:04:42 2023 +0000 +++ b/test-data/ancombc.test1.metadata.tsv Thu Jun 08 19:34:16 2023 +0000 @@ -1,5 +1,5 @@ sample-id barcode-sequence bodysite month day subject animal testcolumn singlecolumn AZcolumn -#q2:types categorical categorical numeric numeric categorical categorical categorical categorical categorical +#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 @@ -34,3 +34,6 @@ 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 9b2a68d3017f -r fe99db171ce5 test-data/ancombc.test1.table.qza Binary file test-data/ancombc.test1.table.qza has changed