Mercurial > repos > public-health-bioinformatics > match_plasmid_to_reference
view 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 |
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date | Tue, 12 Nov 2019 22:47:36 -0500 |
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<tool id="match_plasmid_to_reference" name="Match plasmid to reference" version="0.1.0"> <description>Pick plasmids containing specific genes</description> <requirements> </requirements> <command detect_errors="exit_code"><![CDATA[ '$__tool_directory__/match_plasmid_to_reference.py' --plasmid '${plasmid}' --reference_plasmids_genbank #for $reference_plasmid in $reference_plasmids_genbank: '${reference_plasmid}' #end for --reference_plasmids_fasta #for $reference_plasmid in $reference_plasmids_fasta: '${reference_plasmid}' #end for --mob_typer_report '${concatenated_mob_typer_reports}' --outdir outdir ]]></command> <inputs> <param name="plasmid" type="data" format="fasta" /> <param name="reference_plasmids_genbank" type="data_collection" collection_type="list" format="genbank" /> <param name="reference_plasmids_fasta" type="data_collection" collection_type="list" format="fasta" /> <param name="concatenated_mob_typer_reports" type="data" format="tabular" /> </inputs> <outputs> <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" label="Plasmid" format="fasta"/> <data name="matched_reference_plasmid_genbank" from_work_dir="outdir/reference_plasmid.gbk" label="Reference Plasmid (genbank)" format="genbank"/> <data name="matched_reference_plasmid_fasta" from_work_dir="outdir/reference_plasmid.fasta" label="Reference Plasmid (fasta)" format="fasta"/> <data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" label="Matched MOB-Typer Record" format="tabular"/> </outputs> <tests> <test> <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/> <param name="reference_plasmids_genbank"> <collection type="list"> <element name="CP008719" value="CP008719.gbk" ftype="genbank" /> <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" /> </collection> </param> <param name="reference_plasmids_fasta"> <collection type="list"> <element name="CP008719" value="CP008719.fa" ftype="fasta" /> <element name="JQ739157" value="JQ739157.fa" ftype="fasta" /> </collection> </param> <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" /> <output name="output_plasmid" file="outdir/plasmid.fasta" /> <output name="matched_reference_plasmid_genbank" file="outdir/reference_plasmid.gbk" /> <output name="matched_reference_plasmid_fasta" file="outdir/reference_plasmid.fasta" /> <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" /> </test> </tests> <help><![CDATA[ ]]></help> <citations> </citations> </tool>