| Previous changeset 0:320c9af45b63 (2022-08-29) Next changeset 2:75b07a996ac0 (2023-06-08) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732 |
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modified:
qiime2__demux__emp_single.xml |
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added:
test-data/emp_single.test0.sample-metadata.tsv test-data/emp_single.test0.sequences.qza test-data/summarize.test0.demux.qza |
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removed:
test-data/.gitkeep |
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| diff -r 320c9af45b63 -r 335abb486193 qiime2__demux__emp_single.xml --- a/qiime2__demux__emp_single.xml Mon Aug 29 19:27:37 2022 +0000 +++ b/qiime2__demux__emp_single.xml Fri Jan 13 22:43:21 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 demux emp-single" id="qiime2__demux__emp_single" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 demux emp-single" id="qiime2__demux__emp_single" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> <description>Demultiplex sequence data generated with the EMP protocol.</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 demux</version_command> - <command detect_errors="aggressive">q2galaxy run demux emp_single '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run demux emp_single '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -58,7 +58,30 @@ <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/> <data name="error_correction_details" format="qza" label="${tool.name} on ${on_string}: error_correction_details.qza" from_work_dir="error_correction_details.qza"/> </outputs> - <tests/> + <tests> + <test> + <param name="seqs" value="emp_single.test0.sequences.qza" ftype="qza"/> + <conditional name="barcodes"> + <param name="type" value="tsv"/> + <param name="source" value="emp_single.test0.sample-metadata.tsv" ftype="qiime2.tabular"/> + <param name="column" value="2"/> + </conditional> + <output name="per_sample_sequences" 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"> + <has_line_matching expression="type: SampleData\[SequencesWithQuality\]"/> + </has_archive_member> + </assert_contents> + </output> + <output name="error_correction_details" 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"> + <has_line_matching expression="type: ErrorCorrectionDetails"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: demux emp-single ========================= @@ -76,6 +99,35 @@ ------------ Demultiplex sequence data (i.e., map barcode reads to sample ids) for data generated with the Earth Microbiome Project (EMP) amplicon sequencing protocol. Details about this protocol can be found at http://www.earthmicrobiome.org/protocols-and-standards/ +Examples: +--------- + +demux +***** +Using the ``qiime2 demux emp-single`` tool: + #. Set *"seqs"* to ``#: sequences.qza`` + #. For *"barcodes"*: + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``sample-metadata.tsv`` + #. Set *"Column Name"* to ``barcode-sequence`` + + #. Press the ``Execute`` button. + +Once completed, for each 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 demux emp-single [...] : per_sample_sequences.qza`` + - ``demux.qza`` + * - ``#: qiime2 demux emp-single [...] : error_correction_details.qza`` + - ``demux-details.qza`` + | |
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| diff -r 320c9af45b63 -r 335abb486193 test-data/emp_single.test0.sample-metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emp_single.test0.sample-metadata.tsv Fri Jan 13 22:43:21 2023 +0000 |
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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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| diff -r 320c9af45b63 -r 335abb486193 test-data/emp_single.test0.sequences.qza |
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| Binary file test-data/emp_single.test0.sequences.qza has changed |
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| diff -r 320c9af45b63 -r 335abb486193 test-data/summarize.test0.demux.qza |
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| Binary file test-data/summarize.test0.demux.qza has changed |