--- a/varscan_somatic.xml	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,140 +0,0 @@
-<tool id="varscan_somatic_vcf" name="VarScan Somatic (VCF Output)" version="2.3.5">
-  <description>
-        somatic mutation caller for cancer genomics
-  </description>
-  <requirements>
-  	<requirement type="package" version="2.3.5">VarScan</requirement>
-  </requirements>
-  <command interpreter="perl">
-  	
-	varscan_somatic.pl 
-  	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" 
-  	"NORMAL::$normal" 
-  	"TUMOR::$tumor"
-	"TUMORBAM::$tumorbam"
-  	"OUTPUT::$output"
-        "LOG::$log"
-  	
-	"OPTION::--min-coverage $min_coverage"
-	"OPTION::--min-coverage-normal $min_coverage_normal"
-	"OPTION::--min-coverage-tumor $min_coverage_tumor"
-	
-	"OPTION::--min-var-freq $min_var_freq"
-	"OPTION::--min-freq-for-hom $min_freq_for_hom"
-	
-	"OPTION::--normal-purity $normal_purity"	
-	"OPTION::--tumor-purity $tumor_purity"		
-	
-	"OPTION::--p-value $p_value"	
-	"OPTION::--somatic-p-value $somatic_p_value"	
-
-	"OPTION::--strand-filter $strand_filter"	
-	"OPTION::--validation $validation"	
-	"OPTION::--output-vcf 1"	
-	
-
-  	
-  </command>
-
-  <inputs>
-
-	<param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
-	<param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
-	<param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" />
-
-	<param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
-	<param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
-	<param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
-	
-	<param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
-	<param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
-	
-	<param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
-	<param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
-	
-
-	<param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
-	<param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
-
-	<param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
-	<param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
-	
-  </inputs>
-  <outputs>
-  	<data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
-        <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
-	<!--<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP file)" />
-	<data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL file)" />-->
-	
-
-  </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>
-