comparison match_plasmid_to_reference.xml @ 0:c917ef6807d7 draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
author public-health-bioinformatics
date Tue, 12 Nov 2019 22:47:36 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:c917ef6807d7
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_genbank
9 #for $reference_plasmid in $reference_plasmids_genbank:
10 '${reference_plasmid}'
11 #end for
12 --reference_plasmids_fasta
13 #for $reference_plasmid in $reference_plasmids_fasta:
14 '${reference_plasmid}'
15 #end for
16 --mob_typer_report '${concatenated_mob_typer_reports}'
17 --outdir outdir
18 ]]></command>
19 <inputs>
20 <param name="plasmid" type="data" format="fasta" />
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" />
23 <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
24 </inputs>
25 <outputs>
26 <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" label="Plasmid" format="fasta"/>
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"/>
29 <data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" label="Matched MOB-Typer Record" format="tabular"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/>
34 <param name="reference_plasmids_genbank">
35 <collection type="list">
36 <element name="CP008719" value="CP008719.gbk" ftype="genbank" />
37 <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" />
38 </collection>
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>
46 <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
47 <output name="output_plasmid" file="outdir/plasmid.fasta" />
48 <output name="matched_reference_plasmid_genbank" file="outdir/reference_plasmid.gbk" />
49 <output name="matched_reference_plasmid_fasta" file="outdir/reference_plasmid.fasta" />
50 <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" />
51 </test>
52 </tests>
53 <help><![CDATA[
54 ]]></help>
55 <citations>
56 </citations>
57 </tool>