Mercurial > repos > eiriche > bsmap
comparison parsewig.xml @ 28:781b796c6b9c draft
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| author | eiriche |
|---|---|
| date | Mon, 03 Dec 2012 02:52:49 -0500 |
| parents | |
| children |
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| 27:549ff234f35e | 28:781b796c6b9c |
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| 1 <tool id="parsewig" name="WIG parser"> | |
| 2 <command interpreter="bash"> | |
| 3 parsewig.sh | |
| 4 input=$input | |
| 5 extract=$extract | |
| 6 #if str($selectContext.context) == "yes": | |
| 7 context="$selectContext.cpg,$selectContext.chg,$selectContext.chh" | |
| 8 #end if | |
| 9 depth=$depth | |
| 10 cov_out=$coverage | |
| 11 meth_out=$methylation | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param name="input" format="text" type="data" label="Methylation calling output file" /> | |
| 15 <param name="extract" type="select" label="Which files should be extracted?"> | |
| 16 <option value="m">Methylation</option> | |
| 17 <option value="c">Coverage</option> | |
| 18 <option value="b">Methylation and Coverage</option> | |
| 19 </param> | |
| 20 | |
| 21 <conditional name="selectContext"> | |
| 22 <param name="context" type="select" label="Limit the output to a specific context?"> | |
| 23 <option value="no">No, report all</option> | |
| 24 <option value="yes">Yes</option> | |
| 25 </param> | |
| 26 <when value="no" /> | |
| 27 <when value="yes"> | |
| 28 <param name="cpg" type="boolean" truevalue="cpg" falsevalue="" checked="False" label="report loci in CpG context" /> | |
| 29 <param name="chg" type="boolean" truevalue="chg" falsevalue="" checked="False" label="report loci in CHG context" /> | |
| 30 <param name="chh" type="boolean" truevalue="chh" falsevalue="" checked="False" label="report loci in CHH context" /> | |
| 31 </when> | |
| 32 </conditional> | |
| 33 <param name="depth" type="integer" value="1" label="Minimum sequencing depth to report loci" /> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data name="methylation" format ="wig" label="WIG parser: Methylation"> | |
| 37 <filter>(extract == 'm' or extract == 'b' )</filter> | |
| 38 </data> | |
| 39 <data name="coverage" format ="wig" label="WIG parser: Coverage"> | |
| 40 <filter>(extract == 'c' or extract == 'b' )</filter> | |
| 41 </data> | |
| 42 | |
| 43 </outputs> | |
| 44 <help> | |
| 45 **What it does** | |
| 46 | |
| 47 This is a parser for the output files coming from "Bismark Methylation Caller" or "BSMAP Methylation Caller". The data is parsed into WIGGLE format. | |
| 48 | |
| 49 Other options: | |
| 50 - define context of cytosines should be reported (CpG, CHG, CHH) | |
| 51 - define the minimum sequencing depth (coverage) of cytosines should be reported | |
| 52 | |
| 53 **Output format** | |
| 54 | |
| 55 You get one file for methylation and/or coverage (depending on what you choose under "Which files should be etracted?"). | |
| 56 | |
| 57 The output has the following columns:: | |
| 58 | |
| 59 Column Description | |
| 60 ------ -------------------------------------------------------- | |
| 61 1 cytosine position | |
| 62 2 methylation state (in %) / coverage | |
| 63 (positive value for plus strand / negative value for minus strand) | |
| 64 | |
| 65 </help> | |
| 66 </tool> | |
| 67 |