<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>