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