| Previous changeset 0:e6978c621d70 (2022-08-29) Next changeset 2:bc3a80afa08d (2023-06-08) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 69da7976573cc07a363ac66bdacc9269d7cd3732 |
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modified:
qiime2__emperor__plot.xml |
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added:
test-data/plot.test0.pcoa-result.qza test-data/plot.test0.sample-metadata.tsv test-data/procrustes_plot.test0.bc-pcoa-result.qza test-data/procrustes_plot.test0.sample-metadata.tsv test-data/procrustes_plot.test0.unw-pcoa-result.qza |
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removed:
test-data/.gitkeep |
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| diff -r e6978c621d70 -r 7c9ec8b8b7f8 qiime2__emperor__plot.xml --- a/qiime2__emperor__plot.xml Mon Aug 29 19:49:22 2022 +0000 +++ b/qiime2__emperor__plot.xml Fri Jan 13 22:50:44 2023 +0000 |
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| @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2022, QIIME 2 development team. +Copyright (c) 2023, 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: 2022.8.1) + q2galaxy (version: 2022.11.1) for: - qiime2 (version: 2022.8.1) + qiime2 (version: 2022.11.1) --> -<tool name="qiime2 emperor plot" id="qiime2__emperor__plot" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 emperor plot" id="qiime2__emperor__plot" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> <description>Visualize and Interact with Principal Coordinates Analysis Plots</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.8</container> + <container type="docker">quay.io/qiime2/core:2022.11</container> </requirements> <version_command>q2galaxy version emperor</version_command> - <command detect_errors="aggressive">q2galaxy run emperor plot '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run emperor plot '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -57,7 +57,24 @@ <outputs> <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> </outputs> - <tests/> + <tests> + <test> + <param name="pcoa" value="plot.test0.pcoa-result.qza" ftype="qza"/> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="plot.test0.sample-metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <output name="visualization" ftype="qzv"> + <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"> + <has_line_matching expression="type: Visualization"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: emperor plot ===================== @@ -74,6 +91,35 @@ ------------ Generates an interactive ordination plot where the user can visually integrate sample metadata. +Examples: +--------- + +emperor_plot +************ +Using the ``qiime2 emperor plot`` tool: + #. Set *"pcoa"* to ``#: pcoa-result.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``sample-metadata.tsv`` + + + #. 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 emperor plot [...] : visualization.qzv`` + - ``plot.qzv`` + | |
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| @@ -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 |
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| @@ -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 |
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