Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_galaxy_predictions.xml @ 5:698579246d0d draft

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planemo upload
author jjjjia
date Tue, 21 Aug 2018 17:53:08 -0400
parents fea89c4d5227
children cabceaa239e4
comparison
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4:bd6f5844d60e 5:698579246d0d
1 <tool id="cpo_prediction" name="cpoParser" version="0.1.0"> 1 <tool id="cpo_prediction_parser" name="cpo_prediction_parser" version="0.1.0">
2 <description>this tool parses stuff</description> 2 <description>This tool combines outputs from MLST, ResFinder, PlasmidFinder, Mobsuite, RGI into a TSV for the cpo_prediction workflow</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.23.4">pandas</requirement> 4 <requirement type="package" version="0.23.4">pandas</requirement>
5 <requirement type="package" version="3.6">python</requirement> 5 <requirement type="package" version="3.6">python</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
17 '-s $__tool_directory__/scheme_species_map.tab' 17 '-s $__tool_directory__/scheme_species_map.tab'
18 '-p $plasmidfinder' 18 '-p $plasmidfinder'
19 ]]> 19 ]]>
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <param type="text" name="ID"/> 22 <param type="txt" name="ID"/>
23 <param type="data" name="mlst" format="tabular" /> 23 <param type="data" name="mlst" format="tabular" />
24 <param type="data" name="mobsuitecontig" format="tabular" /> 24 <param type="data" name="mobsuitecontig" format="tabular" />
25 <param type="data" name="mobsuiteaggregate" format="tabular" /> 25 <param type="data" name="mobsuiteaggregate" format="tabular" />
26 <param type="data" name="abricate" format="tabular" /> 26 <param type="data" name="abricate" format="tabular" />
27 <param type="data" name="rgi" format="tabular" /> 27 <param type="data" name="rgi" format="tabular" />
28 <param type="data" name="plasmidfinder" format="tabular" /> 28 <param type="data" name="plasmidfinder" format="tabular" />
29 <param type="text" name="expected"/> 29 <param type="txt" name="expected"/>
30 </inputs> 30 </inputs>
31 <outputs> 31 <outputs>
32 <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/> 32 <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/>
33 <data name="txtSummary" format="text" from_work_dir="summary.txt"/> 33 <data name="txtSummary" format="txt" from_work_dir="summary.txt"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
37 <param name="ID" value="BC11-Kpn005_S2"/> 37 <param name="ID" value="BC11-Kpn005_S2"/>
38 <param name="mlst" value="BC11-Kpn005_S2.mlst"/> 38 <param name="mlst" value="BC11-Kpn005_S2.mlst"/>