# HG changeset patch
# User eugen
# Date 1345033605 14400
# Node ID 35df90c1f4aa9cd963d85a845b42628caa454185
# Parent  5eaa87eeca9aea77eb4d45ac9f5f3ea27fca4f58
Uploaded

diff -r 5eaa87eeca9a -r 35df90c1f4aa bismark_meth_caller.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_meth_caller.xml	Wed Aug 15 08:26:45 2012 -0400
@@ -0,0 +1,57 @@
+<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>
+