Mercurial > repos > public-health-bioinformatics > pick_plasmids_containing_genes
diff pick_plasmids_containing_genes.xml @ 0:62019f5116f8 draft
"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 |
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date | Tue, 12 Nov 2019 22:20:54 -0500 |
parents | |
children | c9129ecc609d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pick_plasmids_containing_genes.xml Tue Nov 12 22:20:54 2019 -0500 @@ -0,0 +1,50 @@ +<tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" version="0.1.0"> + <description>Pick plasmids containing specific genes</description> + <requirements> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + '$__tool_directory__/pick_plasmids_containing_genes.py' + --plasmids + #for $plasmid in $plasmids: + '${plasmid}' + #end for + --concatenated_abricate_reports '${concatenated_abricate_reports}' + --abricate_report_screening_file '${screening_file.fields.path}' + --outdir outdir + ]]></command> + <inputs> + <param name="plasmids" type="data_collection" collection_type="list" format="fasta" /> + <param name="concatenated_abricate_reports" type="data" format="tabular" /> + <param name="screening_file" type="select" format="tabular"> + <options from_data_table="abricate_report_screening_files"> + <validator type="no_options" message="No abricate report screening files are available" /> + </options> + </param> + </inputs> + <outputs> + <collection name="output" type="list" label="Output plasmids"> + <discover_datasets pattern="__name__" format="fasta" directory="outdir" /> + </collection> + </outputs> + <tests> + <test> + <param name="plasmids"> + <collection type="list"> + <element name="SRR9113487_plasmid_1068" value="SRR9113487_plasmid_1068.fasta" ftype="fasta" /> + <element name="SRR9113487_plasmid_1550" value="SRR9113487_plasmid_1550.fasta" ftype="fasta" /> + <element name="SRR9113487_plasmid_2719" value="SRR9113487_plasmid_2719.fasta" ftype="fasta" /> + <element name="SRR9113487_plasmid_739" value="SRR9113487_plasmid_739.fasta" ftype="fasta" /> + <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" /> + <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" /> + </collection> + </param> + <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/> + <param name="screening_file" value="screening_file_1"/> + <output file="outdir/SRR9113487_plasmid_2719.fasta" ftype="fasta"/> + </test> + </tests> + <help><![CDATA[ + ]]></help> + <citations> + </citations> +</tool>