Mercurial > repos > eiriche > bsmap
view parsewig.xml @ 32:117639df067a draft
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author | eiriche |
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date | Mon, 03 Dec 2012 03:10:23 -0500 |
parents | 781b796c6b9c |
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<tool id="parsewig" name="WIG parser"> <command interpreter="bash"> parsewig.sh input=$input extract=$extract #if str($selectContext.context) == "yes": context="$selectContext.cpg,$selectContext.chg,$selectContext.chh" #end if depth=$depth cov_out=$coverage meth_out=$methylation </command> <inputs> <param name="input" format="text" type="data" label="Methylation calling output file" /> <param name="extract" type="select" label="Which files should be extracted?"> <option value="m">Methylation</option> <option value="c">Coverage</option> <option value="b">Methylation and Coverage</option> </param> <conditional name="selectContext"> <param name="context" type="select" label="Limit the output to a specific context?"> <option value="no">No, report all</option> <option value="yes">Yes</option> </param> <when value="no" /> <when value="yes"> <param name="cpg" type="boolean" truevalue="cpg" falsevalue="" checked="False" label="report loci in CpG context" /> <param name="chg" type="boolean" truevalue="chg" falsevalue="" checked="False" label="report loci in CHG context" /> <param name="chh" type="boolean" truevalue="chh" falsevalue="" checked="False" label="report loci in CHH context" /> </when> </conditional> <param name="depth" type="integer" value="1" label="Minimum sequencing depth to report loci" /> </inputs> <outputs> <data name="methylation" format ="wig" label="WIG parser: Methylation"> <filter>(extract == 'm' or extract == 'b' )</filter> </data> <data name="coverage" format ="wig" label="WIG parser: Coverage"> <filter>(extract == 'c' or extract == 'b' )</filter> </data> </outputs> <help> **What it does** This is a parser for the output files coming from "Bismark Methylation Caller" or "BSMAP Methylation Caller". The data is parsed into WIGGLE format. Other options: - define context of cytosines should be reported (CpG, CHG, CHH) - define the minimum sequencing depth (coverage) of cytosines should be reported **Output format** You get one file for methylation and/or coverage (depending on what you choose under "Which files should be etracted?"). The output has the following columns:: Column Description ------ -------------------------------------------------------- 1 cytosine position 2 methylation state (in %) / coverage (positive value for plus strand / negative value for minus strand) </help> </tool>