view mutect_wrapper.xml @ 16:52efdea30175 draft default tip

Fixes. MuTect now works

<tool name="MuTect" id="muTect" version="0.0.1">
  <expand macro="requirements" />
  <macros>
    <import>mutect_macros.xml</import>
  </macros>

  <command interpreter="python">
    mutect_wrapper.py -j '@JAR_PATH@'
	-T MuTect 
	
	#if $genomeSource.refGenomeSource == "history":
 	--ref "${genomeSource.ownFile}"
	#else:
 	--ref "${genomeSource.index.fields.path}"
	#end if
        #if ($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_normal $normal
	##--index_normal ${normal.metadata.bam_index} 
	--input_tumor $tumor
        ##--index_tumor ${normal.metadata.bam_index}
	--callstats $callstats
	--coverage $coverage	
	--vcf $vcf > $logfile

  </command>
  <inputs>
    <param name="normal" type="data" format="bam" label="Normal Tissue BAM file" optional="false"/>
    <param name="tumor" type="data" format="bam" label="Tumor Tissue BAM file" optional="false"/>
	<!-- Reference Fasta -->
    <conditional name="genomeSource"> 
      <param name="refGenomeSource" type="select" label="Select Reference Genome" >
        <option value="indexed">Select a built-in genome</option>
        <option value="history">Use a genome (fasta format) from my history</option>
      </param>
      <when value="indexed">
        <param name="index" type="select" label="Select a built-in reference genome" help="This list contains genomes cached at this Galaxy instance. If your genome of interest is not present here request it by using 'Help' link at the top of Galaxy interface or use the 'Use a genome (fasta format) from my history' option of the 'Select Reference Genome' dropdown.">
          <options from_data_table="all_fasta" />
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome from history" help="This option works best for relatively small genomes. If you are working with large human-sized genomes, send request to Galaxy team for adding your reference to this Galaxy instance by using 'Help' link at the top of Galaxy interface."/>
      </when>
    </conditional>
    <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="bed" label="Intervals to process (BED file)" help="'chr1:1500-2500', one entry per line" optional="true"/>
    	
    <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="MuTect Result (Tabular)" />
	<data format="vcf" name="vcf" label="MuTect Result (VCF)" />
	<data format="wig" name="coverage" label="MuTect Coverage Track (WIG)" />
	<data format="txt" name="logfile" label="MuTect Runtime Output"/>
  </outputs>
  <tests>
  </tests>
  <help>

.. class:: infomark

**Purpose**

Run muTect on paired normal/tumor bam files. Currently, there is support for the default settings. We tried to follow the configuration settings of the GATK wrappers. If you're interested in contributing to these wrappers, feel free to contact me. 

  </help>
</tool>