<tool id="varscan_mpileup" name="VarScan mpileup" version="2.3.5">
  <description>
        mutation caller for targeted, exome, and whole-genome resequencing
  </description>
  <requirements>
  	<requirement type="package" version="2.3.5">VarScan</requirement>
  </requirements>
  <command interpreter="perl">
  	
	varscan_mpileup.pl 
	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar $exe_command" 
  	"INPUT::$in_file"
  	"OUTPUT::$output"
  	"LOG::$log"
	"OPTION::--min-coverage $min_coverage"
	"OPTION::--min-reads2 $min_reads2"
	"OPTION::--min-avg-qual $min_avg_qual"
	"OPTION::--min-var-freq $min_var_freq"
	"OPTION::--min-freq-for-hom $min_freq_for_hom"
	"OPTION::--p-value $p_value"	
	"OPTION::--strand-filter $strand_filter"	
	"OPTION::--output-vcf 1"	
	
	#if ($vcf_sample_list):
		"OPTION::--vcf-sample-list $vcf_sample_list"
	#end if
	"OPTION::--variants $variants"	
	
	
  	
  </command>

  <inputs>
  	
	<param name="exe_command" type="select" label="Command" help="" optional="false">
		<option value="mpileup2snp" >mpileup2snp</option>
		<option value="mpileup2indel">mpileup2indel</option>
		<option value="mpileup2cns">mpileup2cns</option>
	</param>
	<param name="in_file" type="data" format="pileup" label="mpileup file" help="The SAMtools mpileup file" />
	<param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
	<param name="min_reads2" type="integer" label="min-reads2" help="" optional="true" value="2"/>
	<param name="min_avg_qual" type="integer" label="min-avg-qual" help="" optional="true" value="15"/>
	<param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.01"/>
	<param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
	<param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
	<param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
	<param name="vcf_sample_list" type="data" label="vcf-sample-list" format="txt" help="" optional="true" />
	<param name="variants" type="integer" label="variants" help="Set to 1 to report only variants" optional="true" value="1"/>
	
	
  </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) "/>
  </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 file - The SAMtools mpileup file
 

**Parameters**

::

  commands
	mpileup2snp		Identify SNPs from an mpileup file
	mpileup2indel		Identify indels an mpileup file
	mpileup2cns		Call consensus and variants from an mpileup file

  min-coverage	
  	Minimum read depth at a position to make a call [8]

  min-reads2	
  	Minimum supporting reads at a position to call variants [2]

  min-avg-qual	
  	Minimum base quality at a position to count a read [15]

  min-var-freq	
        Minimum variant allele frequency threshold [0.01]

  min-freq-for-hom
  	Minimum frequency to call homozygote [0.75]
  
  p-value
  	Default p-value threshold for calling variants [99e-02]
  
  strand-filter
  	Ignore variants with >90% support on one strand [1]
  
  output-vcf
  	If set to 1, outputs in VCF format
  
  vcf-sample-list
  	For VCF output, a list of sample names in order, one per line
  
  variants
  	Report only variant (SNP/indel) positions [0]


  
  </help>
</tool>