Mercurial > repos > dfornika > match_plasmid_to_reference

comparison match_plasmid_to_reference.xml @ 4:826ddf832bef draft default tip

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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 13:52:40 -0500
parents d56b4f743779
children
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3:d56b4f743779 4:826ddf832bef
3 <requirements> 3 <requirements>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 '$__tool_directory__/match_plasmid_to_reference.py' 6 '$__tool_directory__/match_plasmid_to_reference.py'
7 --plasmid '${plasmid}' 7 --plasmid '${plasmid}'
8 --reference_plasmids 8 --reference_plasmids_genbank
9 #for $reference_plasmid in $reference_plasmids: 9 #for $reference_plasmid in $reference_plasmids_genbank:
10 '${reference_plasmid}'
11 #end for
12 --reference_plasmids_fasta
13 #for $reference_plasmid in $reference_plasmids_fasta:
10 '${reference_plasmid}' 14 '${reference_plasmid}'
11 #end for 15 #end for
12 --mob_typer_report '${concatenated_mob_typer_reports}' 16 --mob_typer_report '${concatenated_mob_typer_reports}'
13 --outdir outdir 17 --outdir outdir
14 ]]></command> 18 ]]></command>
15 <inputs> 19 <inputs>
16 <param name="plasmid" type="data" format="fasta" /> 20 <param name="plasmid" type="data" format="fasta" />
17 <param name="reference_plasmids" type="data_collection" collection_type="list" format="genbank" /> 21 <param name="reference_plasmids_genbank" type="data_collection" collection_type="list" format="genbank" />
22 <param name="reference_plasmids_fasta" type="data_collection" collection_type="list" format="fasta" />
18 <param name="concatenated_mob_typer_reports" type="data" format="tabular" /> 23 <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
19 </inputs> 24 </inputs>
20 <outputs> 25 <outputs>
21 <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" label="Plasmid" format="fasta"/> 26 <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" label="Plasmid" format="fasta"/>
22 <data name="matched_reference_plasmid" from_work_dir="outdir/reference_plasmid.gbk" label="Reference Plasmid" format="genbank"/> 27 <data name="matched_reference_plasmid_genbank" from_work_dir="outdir/reference_plasmid.gbk" label="Reference Plasmid (genbank)" format="genbank"/>
28 <data name="matched_reference_plasmid_fasta" from_work_dir="outdir/reference_plasmid.fasta" label="Reference Plasmid (fasta)" format="fasta"/>
23 <data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" label="Matched MOB-Typer Record" format="tabular"/> 29 <data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" label="Matched MOB-Typer Record" format="tabular"/>
24 </outputs> 30 </outputs>
25 <tests> 31 <tests>
26 <test> 32 <test>
27 <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/> 33 <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/>
28 <param name="reference_plasmids"> 34 <param name="reference_plasmids_genbank">
29 <collection type="list"> 35 <collection type="list">
30 <element name="CP008719" value="CP008719.gbk" ftype="genbank" /> 36 <element name="CP008719" value="CP008719.gbk" ftype="genbank" />
31 <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" /> 37 <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" />
32 </collection> 38 </collection>
33 </param> 39 </param>
40 <param name="reference_plasmids_fasta">
41 <collection type="list">
42 <element name="CP008719" value="CP008719.fa" ftype="fasta" />
43 <element name="JQ739157" value="JQ739157.fa" ftype="fasta" />
44 </collection>
45 </param>
34 <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" /> 46 <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
35 <output name="output_plasmid" file="outdir/plasmid.fasta" /> 47 <output name="output_plasmid" file="outdir/plasmid.fasta" />
36 <output name="matched_reference_plasmid" file="outdir/reference_plasmid.gbk" /> 48 <output name="matched_reference_plasmid_genbank" file="outdir/reference_plasmid.gbk" />
49 <output name="matched_reference_plasmid_fasta" file="outdir/reference_plasmid.fasta" />
37 <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" /> 50 <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" />
38 </test> 51 </test>
39 </tests> 52 </tests>
40 <help><![CDATA[ 53 <help><![CDATA[
41 ]]></help> 54 ]]></help>