Mercurial > repos > alenail > chipsequtil
view chipsequtil/map_to_known_genes.xml @ 6:124231ed2402 draft
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author | alenail |
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date | Mon, 04 Apr 2016 14:56:51 -0400 |
parents | 0eaa8225a09a |
children | a30aa2806375 |
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<tool id="chipsequtil_maptoknowngenes" name="Map Peaks to Known Genes" version="0.1"> <description> Map the peaks in <peaks file> to genes in <knownGene file>. <knownGene file> isformat is as specified in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.sql.<peaks file> format is as produced by MACS. If *auto* is chosen (default) file extension is examined for *.xls* for default MACS format or *.bed* for BED format. If the --detail option is provided, the following extra fields are appended to each row: peak loc, dist from feature, map type, map subtype </description> <parallelism method="basic"></parallelism> <requirements> <requirement type="package" version="1.0">chipsequtil</requirement> </requirements> <command interpreter="python"> map_to_known_genes.py $tss --upstream-window=$upst_win --downstream-window=$dnst_win --map-output=$peaksOutput --peaks-format=$peaks_fmt $detail $intergenic $knownGeneFile $knownGeneRef $macsPeaksFile </command> <inputs> <param name="knownGeneFile" type="data" label="knownGene file" help="" optional="false" /> <param name="knownGeneRef" type="data" label="knownGene xRef file" help="" optional="false" /> <param name="macsPeaksFile" type="data" label="Peaks File" help="" optional="false" /> <param name="peaksOutput" type="text" label="Output filename" help="filename to output mapped peaks to" optional="false" /> <param name="upst_win" type="integer" label="Upstream Window" help="Window width in base pairs to consider promoter region [default: %default]" optional="false" value="5500" /> <param name="dnst_win" type="integer" label="Downstream Window" help="Window width in base pairs to consider downstream region [default: %default]" optional="false" value="2500" /> <param name="tss" checked="true" label="Calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" /> <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false"> <option value="MACS">MACS</option> <option selected="true" value="BED">BED</option> </param> <param name="detail" checked="true" label="Append the following fields to each row: peak loc, dist from feature, map type, map subtype" type="boolean" truevalue="--detail" falsevalue="" help="" /> <param name="intergenic" checked="false" label="Write intergenic peaks to the gene file as well with None as gene ID" type="boolean" truevalue="--intergenic" falsevalue="" help="" /> </inputs> <outputs> <data format="txt" hidden="false" name="default"/> </outputs> <help></help> </tool>