|
5
|
1 <tool id="cpo_tree_drawer" name="cpo_tree_drawer" version="0.1.0">
|
|
|
2 <description>This tool makes a phylogenetic tree using data from snippy alignments, clustalw NJ tree and metadat from cpo_prediction workflow using ETE3</description>
|
|
1
|
3 <requirements>
|
|
|
4 <requirement type="package" version="0.23.4">pandas</requirement>
|
|
|
5 <requirement type="package" version="3.6">python</requirement>
|
|
5
|
6 <requirement type="package" version="3.1.1">ete3</requirement>
|
|
|
7 </requirements>
|
|
1
|
8 <command detect_errors="exit_code">
|
|
|
9 <![CDATA[
|
|
|
10 python '$__tool_directory__/cpo_galaxy_tree.py'
|
|
|
11 '-t $tree'
|
|
|
12 '-d $distance'
|
|
|
13 '-m $metadata'
|
|
|
14 ]]>
|
|
|
15 </command>
|
|
|
16 <inputs>
|
|
|
17 <param type="data" name="tree" format="txt"/>
|
|
|
18 <param type="data" name="distance" format="tabular" />
|
|
|
19 <param type="data" name="metadata" format="tabular" />
|
|
|
20 </inputs>
|
|
|
21 <outputs>
|
|
|
22 <data name="tsvSummary" format="png" from_work_dir="tree.png"/>
|
|
|
23 </outputs>
|
|
|
24 <tests>
|
|
|
25 <test>
|
|
|
26 <param name="ID" value="BC11-Kpn005_S2"/>
|
|
|
27 <param name="mlst" value="BC11-Kpn005_S2.mlst"/>
|
|
|
28 <param name="mobsuitecontig" value="contig_report"/>
|
|
|
29 <param name="mobsuiteaggregate" value="mobtyper_aggregate_report"/>
|
|
|
30 <param name="abricate" value="BC11-Kpn005_S2.cp"/>
|
|
|
31 <param name="rgi" value="BC11-Kpn005_S2.rgi.txt"/>
|
|
|
32 <param name="plasmidfinder" value="BC11-Kpn005_S2.origins"/>
|
|
|
33 <param name="expected" value="Klebsiella pneumoniae"/>
|
|
|
34 <output name="tsvSummary" file="summary.tsv"/>
|
|
|
35 <output name="txtSummary" file="summary.txt"/>
|
|
|
36 </test>
|
|
|
37 </tests>
|
|
|
38 <help>
|
|
|
39 This tool parses stuff.
|
|
|
40 </help>
|
|
|
41 <citations>
|
|
|
42 <citation type="bibtex">
|
|
|
43 @misc{cpo,
|
|
|
44 author = {j, j},
|
|
|
45 year = {2018},
|
|
|
46 title = {cpo_prediction},
|
|
|
47 publisher = {j},
|
|
|
48 journal = {j of j},
|
|
|
49 url = {https://bfjia.net,
|
|
|
50 }</citation>
|
|
|
51 </citations>
|
|
|
52 </tool> |
