Mercurial > repos > dfornika > match_plasmid_to_reference
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 |
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date | Wed, 06 Nov 2019 00:08:43 -0500 |
parents | |
children | 3616b6eda1da |
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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> |