Mercurial > repos > public-health-bioinformatics > match_plasmid_to_reference
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 |
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| date | Tue, 12 Nov 2019 22:47:36 -0500 |
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| -1:000000000000 | 0:c917ef6807d7 |
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| 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> |