|
5
|
1 <tool id="cpo_prediction_parser" name="cpo_prediction_parser" version="0.1.0">
|
|
|
2 <description>This tool combines outputs from MLST, ResFinder, PlasmidFinder, Mobsuite, RGI into a TSV for the cpo_prediction workflow</description>
|
|
|
3 <requirements>
|
|
1
|
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'
|
|
12
|
10 '-i $contig.element_identifier'
|
|
1
|
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>
|
|
12
|
22 <param type="data" name="contig"/>
|
|
1
|
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" />
|
|
13
|
29 <param type="text" name="expected" optional ="false"/>
|
|
1
|
30 </inputs>
|
|
|
31 <outputs>
|
|
|
32 <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/>
|
|
13
|
33 <data name="tsvSummaryExistingFormat" format="tabular" from_work_dir="summary.linda.tsv"/>
|
|
5
|
34 <data name="txtSummary" format="txt" from_work_dir="summary.txt"/>
|
|
1
|
35 </outputs>
|
|
|
36 <tests>
|
|
|
37 <test>
|
|
|
38 <param name="ID" value="BC11-Kpn005_S2"/>
|
|
|
39 <param name="mlst" value="BC11-Kpn005_S2.mlst"/>
|
|
|
40 <param name="mobsuitecontig" value="contig_report"/>
|
|
|
41 <param name="mobsuiteaggregate" value="mobtyper_aggregate_report"/>
|
|
|
42 <param name="abricate" value="BC11-Kpn005_S2.cp"/>
|
|
|
43 <param name="rgi" value="BC11-Kpn005_S2.rgi.txt"/>
|
|
|
44 <param name="plasmidfinder" value="BC11-Kpn005_S2.origins"/>
|
|
|
45 <param name="expected" value="Klebsiella pneumoniae"/>
|
|
|
46 <output name="tsvSummary" file="summary.tsv"/>
|
|
6
|
47 <output name="tsvSummary" file="summary.txt"/>
|
|
1
|
48 </test>
|
|
|
49 </tests>
|
|
|
50 <help>
|
|
|
51 This tool parses stuff.
|
|
|
52 </help>
|
|
|
53 <citations>
|
|
|
54 <citation type="bibtex">
|
|
|
55 @misc{cpo,
|
|
|
56 author = {j, j},
|
|
|
57 year = {2018},
|
|
|
58 title = {cpo_prediction},
|
|
|
59 publisher = {j},
|
|
|
60 journal = {j of j},
|
|
|
61 url = {https://bfjia.net,
|
|
|
62 }</citation>
|
|
|
63 </citations>
|
|
|
64 </tool> |
