Mercurial > repos > jjjjia > cpo_prediction
comparison cpo_galaxy_predictions.xml @ 1:fea89c4d5227 draft
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| author | jjjjia |
|---|---|
| date | Thu, 16 Aug 2018 19:27:05 -0400 |
| parents | |
| children | 698579246d0d |
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| 0:917a05a03ac9 | 1:fea89c4d5227 |
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| 1 <tool id="cpo_prediction" name="cpoParser" version="0.1.0"> | |
| 2 <description>this tool parses stuff</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.23.4">pandas</requirement> | |
| 5 <requirement type="package" version="3.6">python</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"> | |
| 8 <![CDATA[ | |
| 9 python '$__tool_directory__/cpo_galaxy_prediction.py' | |
| 10 '-i $ID' | |
| 11 '-m $mlst' | |
| 12 '-c $mobsuitecontig' | |
| 13 '-f $mobsuiteaggregate' | |
| 14 '-a $abricate' | |
| 15 '-r $rgi' | |
| 16 '-e $expected' | |
| 17 '-s $__tool_directory__/scheme_species_map.tab' | |
| 18 '-p $plasmidfinder' | |
| 19 ]]> | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param type="text" name="ID"/> | |
| 23 <param type="data" name="mlst" format="tabular" /> | |
| 24 <param type="data" name="mobsuitecontig" format="tabular" /> | |
| 25 <param type="data" name="mobsuiteaggregate" format="tabular" /> | |
| 26 <param type="data" name="abricate" format="tabular" /> | |
| 27 <param type="data" name="rgi" format="tabular" /> | |
| 28 <param type="data" name="plasmidfinder" format="tabular" /> | |
| 29 <param type="text" name="expected"/> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/> | |
| 33 <data name="txtSummary" format="text" from_work_dir="summary.txt"/> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="ID" value="BC11-Kpn005_S2"/> | |
| 38 <param name="mlst" value="BC11-Kpn005_S2.mlst"/> | |
| 39 <param name="mobsuitecontig" value="contig_report"/> | |
| 40 <param name="mobsuiteaggregate" value="mobtyper_aggregate_report"/> | |
| 41 <param name="abricate" value="BC11-Kpn005_S2.cp"/> | |
| 42 <param name="rgi" value="BC11-Kpn005_S2.rgi.txt"/> | |
| 43 <param name="plasmidfinder" value="BC11-Kpn005_S2.origins"/> | |
| 44 <param name="expected" value="Klebsiella pneumoniae"/> | |
| 45 <output name="tsvSummary" file="summary.tsv"/> | |
| 46 <output name="txtSummary" file="summary.txt"/> | |
| 47 </test> | |
| 48 </tests> | |
| 49 <help> | |
| 50 This tool parses stuff. | |
| 51 </help> | |
| 52 <citations> | |
| 53 <citation type="bibtex"> | |
| 54 @misc{cpo, | |
| 55 author = {j, j}, | |
| 56 year = {2018}, | |
| 57 title = {cpo_prediction}, | |
| 58 publisher = {j}, | |
| 59 journal = {j of j}, | |
| 60 url = {https://bfjia.net, | |
| 61 }</citation> | |
| 62 </citations> | |
| 63 </tool> |