--- a/bsmap_meth_caller.xml	Mon Dec 03 02:42:04 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-<tool id="bsmap_meth_caller" name="BSMAP Methylation Caller">
-	<requirements>
-	    <requirement type='package' version="2.6">bsmap</requirement>
-	    <requirement type='package'>samtools</requirement>
-        <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>
-