<tool id="bsmap_meth_caller" name="BSMAP Methylation Caller">
	<requirements>
	    <requirement type='package' version="2.6">bsmap</requirement>
	    <requirement type='package'>samtools</requirement>
	</requirements>
        <command interpreter="bash">
               bsmap_meth_caller.sh			
			input=$bsmap_sam
			unique=$unique
			properly=$properly
			zero_meth = $zero_meth
			rem_dup = $rem_dup
			combine_cpg = $combine_cpg
			trimN = $trimN
			depth = $depth			
			output=$output
			tempdir=$output.files_path
			#if $refGenomeSource.genomeSource == "history":
                                ref="${refGenomeSource.myFile}"
                        #else
                                ref="${refGenomeSource.builtinFile.fields.path}"
                        #end if

        </command>
  <inputs>
	<conditional name="refGenomeSource">
      		<param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in reference?" help="Must be the same reference as used for the mapping">
		        <option value="builtin">Use a built-in reference</option>
		        <option value="history">Use one from the history</option>
		</param>
      		<when value="builtin">
		        <param name="builtinFile" type="select" label="Select the reference genome">
				<options from_data_table="bsmap_fasta">
			 		<filter type="sort_by" column="2" />
			                <validator type="no_options" message="No reference genomes are available" />
			        </options>
		        </param>
	        </when>
      		<when value="history">
		        <param name="myFile" type="data" format="fasta" label="Select the reference genome" />
	        </when>
	</conditional>

	<param name="bsmap_sam" format="sam" type="data" label="BSMAP mapping output file" help="Must be in SAM format" />
	<param name="unique" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only unique mappings/pairs" />  
	<param name="properly" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only properly paired mappings" /> 
	<param name="zero_meth" type="boolean" truevalue="true" falsevalue="false" checked="True" label="report loci with zero methylation ratios" /> 
	<param name="rem_dup" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Remove duplicated reads" />
	<param name="combine_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Combine CpG methylaion ratios on both strands" />
	<param name="trimN" type="integer" value="2" label="Trim N fill-in nucleotides in DNA fragment end-repairing" help="This option is only for pair-end mapping. For RRBS, N could be detetmined by the distance between cuttings sites on forward and reverse strands. For WGBS, N is usually between 0~3" />
	<param name="depth" type="integer" value="1" label="Minimum sequencing depth to report loci" />
  </inputs>
  <outputs>
	<data name="output" format ="bed" label="BSMAP methylation output" />
  </outputs>
  <help>
**What it does**

This methylation caller parses the BSMAP SAM output file into bed format.


**Output format** ::


  Column  			Description
  ----------------------	--------------------------------------
  1 chr				chromosome
  2 pos 			position
  3 strand 			strand
  4 context 			context (CHH,CHG,CpG)
  5 coverage 			totally sequenced Cs at that position
  6 methylated			methylated Cs at that position
  7 percentage methylated	percentage of 6
  </help>
</tool>