|
0
|
1 <tool id="abricateCPO" name="abricateCPO" version="0.8">
|
|
|
2 <description>this tool parses stuff</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="0.8">abricate</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command detect_errors="exit_code">
|
|
|
7 <![CDATA[
|
|
|
8 abricate
|
|
|
9 --datadir=$__tool_directory__/
|
|
|
10 --db=cpo
|
|
|
11 '$input'
|
|
|
12 >report.tsv
|
|
|
13 ]]>
|
|
|
14 </command>
|
|
|
15 <inputs>
|
|
|
16 <param type="data" name="input" format="fasta" />
|
|
|
17 </inputs>
|
|
|
18 <outputs>
|
|
|
19 <data name="report" format="tabular" from_work_dir="report.tsv"/>
|
|
|
20 </outputs>
|
|
|
21 <help>
|
|
|
22 abricate with custom database
|
|
|
23 </help>
|
|
|
24 <citations>
|
|
|
25 <citation type="bibtex">
|
|
|
26 @misc{cpo,
|
|
|
27 author = {j, j},
|
|
|
28 year = {2018},
|
|
|
29 title = {cpo_prediction},
|
|
|
30 publisher = {j},
|
|
|
31 journal = {j of j},
|
|
|
32 url = {https://bfjia.net,
|
|
|
33 }</citation>
|
|
|
34 </citations>
|
|
|
35 </tool>
|
