# HG changeset patch # User q2d2 # Date 1673650869 0 # Node ID 96d3a6a511bc758529007019a6e51cc38f60ba5c # Parent 3e34b8065c5244946df82dfe09ada74cb2b8ff5a planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 69da7976573cc07a363ac66bdacc9269d7cd3732 diff -r 3e34b8065c52 -r 96d3a6a511bc qiime2__taxa__collapse.xml --- a/qiime2__taxa__collapse.xml Mon Aug 29 20:29:53 2022 +0000 +++ b/qiime2__taxa__collapse.xml Fri Jan 13 23:01:09 2023 +0000 @@ -1,22 +1,22 @@ - + Collapse features by their taxonomy at the specified level - quay.io/qiime2/core:2022.8 + quay.io/qiime2/core:2022.11 q2galaxy version taxa - q2galaxy run taxa collapse '$inputs' + q2galaxy run taxa collapse '$inputs' @@ -38,7 +38,20 @@ - + + + + + + + + + + + + + + QIIME 2: taxa collapse ====================== @@ -55,6 +68,29 @@ ------------ Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. +Examples: +--------- + +collapse +******** +Using the ``qiime2 taxa collapse`` tool: + #. Set *"table"* to ``#: table.qza`` + #. Set *"taxonomy"* to ``#: taxonomy.qza`` + #. Set *"level"* to ``6`` + #. 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 taxa collapse [...] : collapsed_table.qza`` + - ``collapsed-table-l6.qza`` + | diff -r 3e34b8065c52 -r 96d3a6a511bc test-data/.gitkeep diff -r 3e34b8065c52 -r 96d3a6a511bc test-data/barplot.test0.sample-metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barplot.test0.sample-metadata.tsv Fri Jan 13 23:01:09 2023 +0000 @@ -0,0 +1,36 @@ +sample-id barcode-sequence body-site year month day subject reported-antibiotic-usage days-since-experiment-start +#q2:types categorical categorical numeric numeric numeric categorical categorical numeric +L1S8 AGCTGACTAGTC gut 2008 10 28 subject-1 Yes 0 +L1S57 ACACACTATGGC gut 2009 1 20 subject-1 No 84 +L1S76 ACTACGTGTGGT gut 2009 2 17 subject-1 No 112 +L1S105 AGTGCGATGCGT gut 2009 3 17 subject-1 No 140 +L2S155 ACGATGCGACCA left palm 2009 1 20 subject-1 No 84 +L2S175 AGCTATCCACGA left palm 2009 2 17 subject-1 No 112 +L2S204 ATGCAGCTCAGT left palm 2009 3 17 subject-1 No 140 +L2S222 CACGTGACATGT left palm 2009 4 14 subject-1 No 168 +L3S242 ACAGTTGCGCGA right palm 2008 10 28 subject-1 Yes 0 +L3S294 CACGACAGGCTA right palm 2009 1 20 subject-1 No 84 +L3S313 AGTGTCACGGTG right palm 2009 2 17 subject-1 No 112 +L3S341 CAAGTGAGAGAG right palm 2009 3 17 subject-1 No 140 +L3S360 CATCGTATCAAC right palm 2009 4 14 subject-1 No 168 +L5S104 CAGTGTCAGGAC tongue 2008 10 28 subject-1 Yes 0 +L5S155 ATCTTAGACTGC tongue 2009 1 20 subject-1 No 84 +L5S174 CAGACATTGCGT tongue 2009 2 17 subject-1 No 112 +L5S203 CGATGCACCAGA tongue 2009 3 17 subject-1 No 140 +L5S222 CTAGAGACTCTT tongue 2009 4 14 subject-1 No 168 +L1S140 ATGGCAGCTCTA gut 2008 10 28 subject-2 Yes 0 +L1S208 CTGAGATACGCG gut 2009 1 20 subject-2 No 84 +L1S257 CCGACTGAGATG gut 2009 3 17 subject-2 No 140 +L1S281 CCTCTCGTGATC gut 2009 4 14 subject-2 No 168 +L2S240 CATATCGCAGTT left palm 2008 10 28 subject-2 Yes 0 +L2S309 CGTGCATTATCA left palm 2009 1 20 subject-2 No 84 +L2S357 CTAACGCAGTCA left palm 2009 3 17 subject-2 No 140 +L2S382 CTCAATGACTCA left palm 2009 4 14 subject-2 No 168 +L3S378 ATCGATCTGTGG right palm 2008 10 28 subject-2 Yes 0 +L4S63 CTCGTGGAGTAG right palm 2009 1 20 subject-2 No 84 +L4S112 GCGTTACACACA right palm 2009 3 17 subject-2 No 140 +L4S137 GAACTGTATCTC right palm 2009 4 14 subject-2 No 168 +L5S240 CTGGACTCATAG tongue 2008 10 28 subject-2 Yes 0 +L6S20 GAGGCTCATCAT tongue 2009 1 20 subject-2 No 84 +L6S68 GATACGTCCTGA tongue 2009 3 17 subject-2 No 140 +L6S93 GATTAGCACTCT tongue 2009 4 14 subject-2 No 168 diff -r 3e34b8065c52 -r 96d3a6a511bc test-data/barplot.test0.table.qza Binary file test-data/barplot.test0.table.qza has changed diff -r 3e34b8065c52 -r 96d3a6a511bc test-data/barplot.test0.taxonomy.qza Binary file test-data/barplot.test0.taxonomy.qza has changed diff -r 3e34b8065c52 -r 96d3a6a511bc test-data/collapse.test0.table.qza Binary file test-data/collapse.test0.table.qza has changed diff -r 3e34b8065c52 -r 96d3a6a511bc test-data/collapse.test0.taxonomy.qza Binary file test-data/collapse.test0.taxonomy.qza has changed