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comparison pick_plasmids_containing_genes.xml @ 0:62019f5116f8 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
author public-health-bioinformatics
date Tue, 12 Nov 2019 22:20:54 -0500
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children c9129ecc609d
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-1:000000000000 0:62019f5116f8
1 <tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" 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__/pick_plasmids_containing_genes.py'
7 --plasmids
8 #for $plasmid in $plasmids:
9 '${plasmid}'
10 #end for
11 --concatenated_abricate_reports '${concatenated_abricate_reports}'
12 --abricate_report_screening_file '${screening_file.fields.path}'
13 --outdir outdir
14 ]]></command>
15 <inputs>
16 <param name="plasmids" type="data_collection" collection_type="list" format="fasta" />
17 <param name="concatenated_abricate_reports" type="data" format="tabular" />
18 <param name="screening_file" type="select" format="tabular">
19 <options from_data_table="abricate_report_screening_files">
20 <validator type="no_options" message="No abricate report screening files are available" />
21 </options>
22 </param>
23 </inputs>
24 <outputs>
25 <collection name="output" type="list" label="Output plasmids">
26 <discover_datasets pattern="__name__" format="fasta" directory="outdir" />
27 </collection>
28 </outputs>
29 <tests>
30 <test>
31 <param name="plasmids">
32 <collection type="list">
33 <element name="SRR9113487_plasmid_1068" value="SRR9113487_plasmid_1068.fasta" ftype="fasta" />
34 <element name="SRR9113487_plasmid_1550" value="SRR9113487_plasmid_1550.fasta" ftype="fasta" />
35 <element name="SRR9113487_plasmid_2719" value="SRR9113487_plasmid_2719.fasta" ftype="fasta" />
36 <element name="SRR9113487_plasmid_739" value="SRR9113487_plasmid_739.fasta" ftype="fasta" />
37 <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" />
38 <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" />
39 </collection>
40 </param>
41 <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/>
42 <param name="screening_file" value="screening_file_1"/>
43 <output file="outdir/SRR9113487_plasmid_2719.fasta" ftype="fasta"/>
44 </test>
45 </tests>
46 <help><![CDATA[
47 ]]></help>
48 <citations>
49 </citations>
50 </tool>