Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_galaxy_predictions.xml @ 18:596bf8a792de draft

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planemo upload
author jjjjia
date Tue, 28 Aug 2018 15:15:09 -0400
parents a14b12a71a53
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17:ed3b291693fc 18:596bf8a792de
9 python '$__tool_directory__/cpo_galaxy_prediction.py' 9 python '$__tool_directory__/cpo_galaxy_prediction.py'
10 '-i $contig.element_identifier' 10 '-i $contig.element_identifier'
11 '-m $mlst' 11 '-m $mlst'
12 '-c $mobsuitecontig' 12 '-c $mobsuitecontig'
13 '-f $mobsuiteaggregate' 13 '-f $mobsuiteaggregate'
14 '-a $abricate' 14 '-a $resfinder'
15 '-r $rgi' 15 '-r $rgi'
16 '-e $expected' 16 '-e $expected'
17 '-s $__tool_directory__/scheme_species_map.tab' 17 '-s $__tool_directory__/scheme_species_map.tab'
18 '-p $plasmidfinder' 18 '-p $plasmidfinder'
19 '-d $mash'
19 ]]> 20 ]]>
20 </command> 21 </command>
21 <inputs> 22 <inputs>
22 <param type="data" name="contig"/> 23 <param type="data" name="contig"/>
23 <param type="data" name="mlst" format="tabular" /> 24 <param type="data" name="mlst" format="tabular" />
24 <param type="data" name="mobsuitecontig" format="tabular" /> 25 <param type="data" name="mobsuitecontig" format="tabular" />
25 <param type="data" name="mobsuiteaggregate" format="tabular" /> 26 <param type="data" name="mobsuiteaggregate" format="tabular" />
26 <param type="data" name="abricate" format="tabular" /> 27 <param type="data" name="resfinder" format="tabular" />
27 <param type="data" name="rgi" format="tabular" /> 28 <param type="data" name="rgi" format="tabular" />
28 <param type="data" name="plasmidfinder" format="tabular" /> 29 <param type="data" name="plasmidfinder" format="tabular" />
30 <param type="data" name="mash" format ="tabular"/>
29 <param type="text" name="expected" optional ="false"/> 31 <param type="text" name="expected" optional ="false"/>
30 </inputs> 32 </inputs>
31 <outputs> 33 <outputs>
32 <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/> 34 <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/>
33 <data name="tsvSummaryExistingFormat" format="tabular" from_work_dir="summary.linda.tsv"/> 35 <data name="tsvSummaryExistingFormat" format="tabular" from_work_dir="summary.linda.tsv"/>
34 <data name="txtSummary" format="txt" from_work_dir="summary.txt"/> 36 <data name="txtSummary" format="txt" from_work_dir="summary.txt"/>
35 </outputs> 37 </outputs>
36 <tests> 38 <tests>
37 <test> 39 <test>
38 <param name="ID" value="BC11-Kpn005_S2"/> 40 <param name="ID" value="BC11-Kpn005_S2"/>
39 <param name="mlst" value="BC11-Kpn005_S2.mlst"/> 41 <param name="mlst" value="BC11-Kpn005_S2.mlst"/>