Mercurial > repos > dfornika > match_plasmid_to_reference

comparison match_plasmid_to_reference.xml @ 2:faf74a1bbd5f draft

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"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 01:08:56 -0500
parents 3616b6eda1da
children d56b4f743779
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1:3616b6eda1da 2:faf74a1bbd5f
7 --plasmid '${plasmid}' 7 --plasmid '${plasmid}'
8 --reference_plasmids 8 --reference_plasmids
9 #for $reference_plasmid in $reference_plasmids: 9 #for $reference_plasmid in $reference_plasmids:
10 '${reference_plasmid}' 10 '${reference_plasmid}'
11 #end for 11 #end for
12 --concatenated_mob_typer_reports '${concatenated_mob_typer_reports}' 12 --mob_typer_report '${concatenated_mob_typer_reports}'
13 --outdir outdir 13 --outdir outdir
14 ]]></command> 14 ]]></command>
15 <inputs> 15 <inputs>
16 <param name="plasmid" type="data" format="fasta" /> 16 <param name="plasmid" type="data" format="fasta" />
17 <param name="reference_plasmids" type="data_collection" collection_type="list" format="genbank" /> 17 <param name="reference_plasmids" type="data_collection" collection_type="list" format="genbank" />
18 <param name="concatenated_mob_typer_reports" type="data" format="tabular" /> 18 <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
19 </inputs> 19 </inputs>
20 <outputs> 20 <outputs>
21 <data name="plasmid" from_work_dir="outdir/plasmid.fasta" /> 21 <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" />
22 <data name="matched_reference_plasmid" from_work_dir="outdir/reference_plasmid.gbk" /> 22 <data name="matched_reference_plasmid" from_work_dir="outdir/reference_plasmid.gbk" />
23 <data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" /> 23 <data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" />
24 </outputs> 24 </outputs>
25 <tests> 25 <tests>
26 <test> 26 <test>
27 <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/> 27 <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/>
28 <param name="reference_plasmids"> 28 <param name="reference_plasmids">
29 <collection type="list"> 29 <collection type="list">
30 <element name="CP008719.gbk" value="CP008719.gbk" ftype="genbank" /> 30 <element name="CP008719" value="CP008719.gbk" ftype="genbank" />
31 <element name="CP008719.gbk" value="CP008719.gbk" ftype="genbank" /> 31 <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" />
32 </collection> 32 </collection>
33 </param> 33 </param>
34 <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" /> 34 <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
35 <output name="plasmid" file="outdir/plasmid.fasta" /> 35 <output name="output_plasmid" file="outdir/plasmid.fasta" />
36 <output name="reference_plasmid" file="outdir/reference_plasmid.gbk" /> 36 <output name="matched_reference_plasmid" file="outdir/reference_plasmid.gbk" />
37 <output name="mob_typer_record" file="outdir/mob_typer_record.gbk" /> 37 <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" />
38 </test> 38 </test>
39 </tests> 39 </tests>
40 <help><![CDATA[ 40 <help><![CDATA[
41 ]]></help> 41 ]]></help>
42 <citations> 42 <citations>