<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>