|
0
|
1 <tool id="rgi" name="rgi" version="4.0.3">
|
|
|
2 <requirements>
|
|
|
3 <requirement type="package" version="4.0.3">rgi</requirement>
|
|
|
4 <requirement type="package" version="2.7">python</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command detect_errors="exit_code"><![CDATA[
|
|
|
7 wget -O $__tool_directory__/card-data.tar.gz2 https://card.mcmaster.ca/latest/data && tar xjf $__tool_directory__/card-data.tar.gz2 -C $__tool_directory__/ && rgi load -i $__tool_directory__/card.json --local && rgi main -t contig -a BLAST -i $input -o rgiResult -n "\${GALAXY_SLOTS:-4}" --local --clean
|
|
|
8
|
|
|
9 ]]></command>
|
|
|
10
|
|
|
11 <inputs>
|
|
|
12 <param type="data" name="input" format="fasta" />
|
|
|
13 </inputs>
|
|
|
14 <outputs>
|
|
|
15 <data name="rgiResultTsv" format="tabular" from_work_dir="rgiResult.txt"/>
|
|
|
16 </outputs>
|
|
|
17 <help>
|
|
|
18 runs rgi
|
|
|
19 </help>
|
|
|
20 <citations>
|
|
|
21 <citation type="bibtex">
|
|
|
22 @misc{cpo,
|
|
|
23 author = {j, j},
|
|
|
24 year = {2018},
|
|
|
25 title = {cpo_prediction},
|
|
|
26 publisher = {j},
|
|
|
27 journal = {j of j},
|
|
|
28 url = {https://bfjia.net,
|
|
|
29 }</citation>
|
|
|
30 </citations>
|
|
|
31 </tool>
|
