view bismark_meth_caller.xml @ 14:120a27b53be7 draft

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<tool id="bismark_meth_caller" name="Bismark Methylation Caller">
         <requirements>
	    <requirement type="package">
		Bismark
	    </requirement>
	</requirements>
        <command interpreter="bash">
               bismark_meth_caller.sh			
			input=$bismark_sam
			method=$single_paired
			output=$output
			tempdir=$output.files_path
			
        </command>
  <inputs>
	<param name="single_paired" type="select" label="Please select whether Reads are single-end or paired-end">
	    <option value="s">Single-end</option>
	    <option value="p">Paired-end</option>
	</param>
	<param format="sam" name="bismark_sam" type="data" label="Bismark mapping output file" help="Must be in SAM format"/>   
  </inputs>
  <outputs>
	<data name="output" format ="bed" label="Bismark methylation output" />
  </outputs>
  <tests>
    <test>
      <param name="bismark_sam" value="bismark_mapped_reads_single.sam" ftype="sam"/>
      <param name="single_paired" value="s"/>
      <output name="output" file="bismark_methylation_output_single.bed"/>      
    </test>
    <test>
      <param name="bismark_sam" value="bismark_mapped_reads_single.sam" ftype="sam"/>
      <param name="single_paired" value="p"/>
      <output name="output" file="bismark_methylation_output_paired.bed"/>      
    </test>       
  </tests>
  <help>
**What it does**

This methylation caller parses the Bismark SAM output file into bed format. You only need to specify whether the reads are single-end or paired-end


**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>