<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>