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view tools/refseq_parser/refseq_parser.xml @ 0:45533fb9d2f4 draft default tip
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author | matnguyen |
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date | Tue, 04 Sep 2018 02:49:49 -0400 |
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<tool id="parse_refseq_masher" name="Parse refseq_masher matches collection" version="0.1.0"> <description>and output a list of outliers</description> <requirements> <requirement type="package" version="3.1.1">ete3</requirement> </requirements> <command><![CDATA[ $__tool_directory__/refseq_parser $db $taxid #for $report in $reports# $report #end for# ]]></command> <inputs> <param name="db" type="data" format="sqlite" label="(ETE3) Taxonomy Database"/> <param name="reports" type="data" format="tabular" label="Refseq_masher report" help="" optional="false" multiple="True" /> <param name="taxid" type="integer" value="0" label="Taxonomic ID of target taxonomic rank" optional="false"/> </inputs> <outputs> <data name="output_file" label="Outliers from dataset" format="txt" from_work_dir="outlier_list.txt"/> </outputs> <tests> <test> <param name="report" value="test.tsv" ftype="tabular" /> <output name="output" value="output.tsv" ftype="tabular" /> </test> </tests> <help><![CDATA[ Parses refseq_masher output and returns a list of outliers based on two criteria: 1. If the mash match is not the same or a descendant of the target taxonomic ID 2. If the distance between the match and the sample is >0.05 Command line: refseq_parser <ETE3 taxonomy database> <taxid> [input refseq_masher reports ...] ]]></help> <citations> Manuscript in preparation </citations> </tool>