Mercurial > repos > q2d2 > qiime2__demux__tabulate_read_counts
changeset 0:05d47d652efb draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
| author | q2d2 |
|---|---|
| date | Thu, 25 Apr 2024 20:56:11 +0000 |
| parents | |
| children | 028492b9d028 |
| files | qiime2__demux__tabulate_read_counts.xml test-data/emp_single.test0.sample-metadata.tsv test-data/emp_single.test0.sequences.qza test-data/summarize.test0.demux.qza |
| diffstat | 4 files changed, 95 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__demux__tabulate_read_counts.xml Thu Apr 25 20:56:11 2024 +0000 @@ -0,0 +1,59 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2024, 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: 2024.2.1) +for: + qiime2 (version: 2024.2.0) +--> +<tool name="qiime2 demux tabulate-read-counts" id="qiime2__demux__tabulate_read_counts" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> + <description>Tabulate counts per sample</description> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> + </requirements> + <version_command>q2galaxy version demux</version_command> + <command detect_errors="exit_code">q2galaxy run demux tabulate_read_counts '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <param name="sequences" type="data" format="qza" label="sequences: List[SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]]" help="[required] One or more collections of demultiplexed sequences." multiple="true"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="SampleData[SequencesWithQuality]"/> + <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> + <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/> + </options> + </param> + </inputs> + <outputs> + <data name="counts" format="qza" label="${tool.name} on ${on_string}: counts.qza" from_work_dir="counts.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: demux tabulate-read-counts +=================================== +Tabulate counts per sample + + +Outputs: +-------- +:counts.qza: <no description> + +| + +Description: +------------ +Generate a per-sample count of sequence reads. + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emp_single.test0.sample-metadata.tsv Thu Apr 25 20:56:11 2024 +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