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parsewig.xml |
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| diff -r 549ff234f35e -r 781b796c6b9c parsewig.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parsewig.xml Mon Dec 03 02:52:49 2012 -0500 |
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| @@ -0,0 +1,67 @@ +<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> + |