| Previous changeset 0:9b2a68d3017f (2023-01-13) Next changeset 2:3bdf127442ed (2024-04-25) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 65e4952f33eb335528e8553150e9097e5ea8f556 |
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modified:
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 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 |
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| @@ -6,14 +6,14 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2022.11.1) + q2galaxy (version: 2023.5.0) for: - qiime2 (version: 2022.11.1) + qiime2 (version: 2023.5.1) --> -<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"> +<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> <description>Analysis of Composition of Microbiomes with Bias Correction</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.11</container> + <container type="docker">quay.io/qiime2/core:2023.5</container> </requirements> <version_command>q2galaxy version composition</version_command> <command detect_errors="exit_code">q2galaxy run composition ancombc '$inputs'</command> @@ -21,7 +21,7 @@ <inputs name="inputs" data_style="paths"/> </configfiles> <inputs> - <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table to be used for ANCOM computation."> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table to be used for ANCOM-BC computation."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureTable[Frequency]"/> </options> @@ -104,10 +104,13 @@ <param name="source" value="ancombc.test1.metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> - <param name="formula" value="bodysite + month"/> + <param name="formula" value="bodysite + animal"/> <repeat name="reference_levels"> <param name="element" value="bodysite::tongue"/> </repeat> + <repeat name="reference_levels"> + <param name="element" value="animal::dog"/> + </repeat> <output name="differentials" ftype="qza"> <assert_contents> <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"> @@ -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 @@ </help> <citations> - <citation type="doi">10.3402/mehd.v26.27663</citation> + <citation type="doi">10.1038/s41467-020-17041-7</citation> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool> |
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| 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 |
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| @@ -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 |
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| diff -r 9b2a68d3017f -r fe99db171ce5 test-data/ancombc.test0.table.qza |
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| Binary file test-data/ancombc.test0.table.qza has changed |
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| 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 |
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| @@ -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 |
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| diff -r 9b2a68d3017f -r fe99db171ce5 test-data/ancombc.test1.table.qza |
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| Binary file test-data/ancombc.test1.table.qza has changed |