--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/varscan_processSomatic.xml	Fri Mar 07 06:17:32 2014 -0500
@@ -0,0 +1,154 @@
+<tool id="varscan_processSomatic" name="ProcessSomatic" version="2.3.5">
+  <description>
+        Extract HC calls from Somatic Caller
+  </description>
+  <requirements>
+  	<requirement type="package" version="2.3.5">VarScan</requirement>
+  </requirements>
+  <command interpreter="perl">
+  	
+	varscan_processSomatic.pl 
+  	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar processSomatic" 
+	"INPUT::$input"
+        "LOG::$log"
+  	
+	"OPTION::--min-tumor-freq $min_tumor_freq"
+	"OPTION::--max-normal-freq $max_normal_freq"
+	"OPTION::--p-value $p_value"
+	"OUTPUT::--loh $loh"
+	"OUTPUT::--loh_hc $loh_hc"
+	"OUTPUT::--germ $germ"
+	"OUTPUT::--germ_hc $germ_hc"
+	"OUTPUT::--som $som"
+	"OUTPUT::--som_hc $som_hc"
+	"OUTPUT::--som_hc_vcf $som_hc_vcf"
+	"OUTPUT::--germ_hc_vcf $germ_hc_vcf"
+	"OUTPUT::--loh_hc_vcf $loh_hc_vcf"
+	
+  </command>
+
+  <inputs>
+
+	<param name="input" type="data" format="txt" label="Input File" help="VarScan Somatics output file in native format" />
+
+	<param name="min_tumor_freq" type="float" label="min-tumor-freq" help="Minimum variant allele frequency in tumor" optional="true" value="0.10"/>
+	<param name="max_normal_freq" type="float" label="max-normal-freq" help="Maximum variant allele frequency in normal" optional="true" value="0.05"/>
+	<param name="p_value" type="text" label="p-value" help="P-value for high-confidence calling" optional="true" value="0.07"/>
+	<param name="outtype" type="select" label="Output Type:" default="1">
+		<option value="0">Native VarScan Tables</option>
+		<option value="1">VCF format (only High Confidence)</option>
+		<option value="2">Both</option>
+	</param>
+
+  </inputs>
+  <outputs>
+        <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) " />
+        <data type="data" format="txt" name="loh" label="${tool.name} result on ${on_string} (loh) " >
+		<filter>outtype != "1"</filter>
+	</data>
+	<data type="data" format="txt" name="loh_hc" label="${tool.name} result on ${on_string} (loh_hc)">
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="txt" name="germ" label="${tool.name} result on ${on_string} (germline)" >
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="txt" name="germ_hc" label="${tool.name} result on ${on_string} (germline_hc)">
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="txt" name="som" label="${tool.name} result on ${on_string} (somatic)" >
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="txt" name="som_hc" label="${tool.name} result on ${on_string} (somatic_hc)" >
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="vcf" name="som_hc_vcf" label="${tool.name} result on ${on_string} (Somatic_HC.vcf)" >
+		<filter>outtype != "0"</filter>
+	</data>
+
+	<data type="data" format="vcf" name="loh_hc_vcf" label="${tool.name} result on ${on_string} (LOH_HC.vcf)" >
+		<filter>outtype != "0"</filter>
+	</data>
+
+	<data type="data" format="vcf" name="germ_hc_vcf" label="${tool.name} result on ${on_string} (Germline_HC.vcf)" >
+		<filter>outtype != "0"</filter>
+	</data>
+
+
+	
+
+  </outputs>
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+::
+
+ VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
+
+    Germline variants (SNPs an dindels) in individual samples or pools of samples.
+    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
+    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
+    Somatic copy number alterations (CNAs) in tumor-normal exome data.
+
+
+**Input**
+
+::
+
+  mpileup normal file - The SAMtools mpileup file for normal
+  mpileup tumor file - The SAMtools mpileup file for tumor
+ 
+
+**Parameters**
+
+::
+
+  min-coverage	
+  	Minimum read depth at a position to make a call [8]
+
+  min-coverage-normal	
+  	Minimum coverage in normal to call somatic [8]
+  	
+  min-coverage-tumor	
+  	Minimum coverage in tumor to call somatic [6]
+  	
+  min-var-freq 
+  	Minimum variant frequency to call a heterozygote [0.10]  	  	
+
+  min-freq-for-hom
+  	Minimum frequency to call homozygote [0.75]
+  	
+  normal-purity 
+  	Estimated purity (non-tumor content) of normal sample [1.00]
+  	
+  tumor-purity
+  	Estimated purity (tumor content) of tumor sample [1.00]
+  
+  p-value
+  	Default p-value threshold for calling variants [0.99]
+  	
+  somatic-p-value
+  	P-value threshold to call a somatic site [0.05]  	
+  
+  strand-filter
+  	If set to 1, removes variants with >90% strand bias
+  	
+  validation 
+  	If set to 1, outputs all compared positions even if non-variant
+  
+  output-vcf
+  	If set to 1, outputs in VCF format [Default]
+
+
+  
+  </help>
+</tool>
+