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<tool id="muTect" name="muTect" version="1.0.0">
  <description>identify somatic point mutations</description>
  <requirements>
  		<requirement type="set_environment">MUTECTPATH</requirement>
  </requirements>
  <command interpreter="java">
  	-Xmx2g -jar \$MUTECTPATH/muTect-1.1.1.jar
  	--analysis_type MuTect
  	--reference_sequence $reference
  	#if ($cosmic.has_cosmic):
  		--cosmic $cosmic.cosmicfile
  	#end if
	--dbsnp $dbsnp
	#if str($intervals) != "" 
  		--intervals $intervals
  	#end if
  	#if str($intervals) == "" and str($intervalfile) != "" 
  		--intervals $intervalfile
  	#end if
	--input_file:normal $normal
	--input_file:tumor $tumor
	--out call_stats.txt
	--coverage_file coverage.wig.txt	
  </command>

  <inputs>
  	<param name="reference" type="data" format="bed, fasta" label="Select a reference genome">
	</param>
  	<param name="dbsnp" type="data" format="vcf" label="dbsnp.vcf file" />
  	<param name="intervals" type="text" label="Intervals to process" help="In format 'chr1:1500-2500; chr2:2500-3500', separated by semicolons" optional="true"/>
  	<param name="intervalfile" type="data" format="txt" label="Intervals to process (.txt file)" help="'chr1:1500-2500', one entry per line" optional="true"/>
  	<param name="normal" type="data" format="bam" label="Normal BAM file"/>
  	<param name="tumor" type="data" format="bam" label="Tumor BAM file"/>	
    <conditional name="cosmic">
		<param name="has_cosmic" type="boolean" label="Cosmic vcf file available for specimen" value="false" />
		<when value="true">
			<param name="cosmicfile" type="data" format="vcf" label="Cosmic vcf file"/>
		</when>
	</conditional>
    	
    	
  </inputs>
  
  <outputs>
	<data format="txt" name="callstats" label="Detailed caller output" from_work_dir="call_stats.txt"/>
	<data format="txt" name="coverage" label="Filename for coverage output" from_work_dir="coverage.wig.txt"/>
  </outputs>


  <help> 

.. class:: infomark

**License**

TmuTect Revision: 44830
GATK Revision: 2.1-202-g2fe6a31
Copyright (c) 2012 The Broad Institute
Please view our documentation at http://www.broadinstitute.org/gsa/wiki
For support, please view our support site at http://getsatisfaction.com/gsa

**What it does**

MuTect is a method developed at the Broad Institute for the reliable 
and accurate identification of somatic point mutations in next generation 
sequencing data of cancer genomes.



**Input**

Reference Genome:

	Fasta file of ref gnome

Normal Sample:

	bam normal sample

Tumor Sample:

	bam tumor sample


Intervals:

	A list of genomic intervals over which to operate.
	


**Output**

Caller Output: 
	
	Detailed caller output

Coverage Output:
	
	write out coverage in WIGGLE format to this file


  </help>
</tool>