comparison match_plasmid_to_reference.xml @ 0:8bb674372911 draft

"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Wed, 06 Nov 2019 00:08:43 -0500
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children 3616b6eda1da
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-1:000000000000 0:8bb674372911
1 <tool id="match_plasmid_to_reference" name="Match plasmid to reference" version="0.1.0">
2 <description>Pick plasmids containing specific genes</description>
3 <requirements>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 '$__tool_directory__/match_plasmid_to_reference.py'
7 --plasmid '${plasmid}'
8 --reference_plasmids
9 #for $reference_plasmid in $reference_plasmids:
10 '${reference_plasmid}'
11 #end for
12 --concatenated_mob_typer_reports '${concatenated_mob_typer_reports}'
13 --outdir outdir
14 ]]></command>
15 <inputs>
16 <param name="plasmid" type="data" format="fasta" />
17 <param name="reference_plasmids" type="data_collection" collection_type="list" format="genbank" />
18 <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
19 </inputs>
20 <outputs>
21 <data name="plasmid" from_work_dir="outdir/plasmid.fasta" />
22 <data name="reference_plasmid" from_work_dir="outdir/reference_plasmid.gbk" />
23 <data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" />
24 </outputs>
25 <tests>
26 </tests>
27 <help><![CDATA[
28 ]]></help>
29 <citations>
30 </citations>
31 </tool>