<macros>
  <macro name="main">
    <description>Strelka</description>
    <requirements>
      <requirement type="set_environment">SCRIPT_PATH_STRELKA</requirement>
      <requirement type="package" version="0.1.18">samtools</requirement>
      <requirement type="package" version="0.1.11">vcftools</requirement>
    </requirements>
    <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam 
	#silent sys.stderr.write("!!!! Cheetah Template Variables !!!!\n")
	#for k,v in $searchList[2].items()
	#silent   sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))
	#end for
	#silent sys.stderr.write("!!!! end-of-list !!!!\n")     
	#import string

     --scriptPath				\$SCRIPT_PATH_STRELKA
     #if $genomeSource.refGenomeSource == "history":
      --refFile "${genomeSource.ownFile}"
     #else:
      --refFile "${genomeSource.index.fields.path}"
     #end if   

     #if $configuration.configuration_switch == 'Default for Bwa':
    --configFile 				strelka_config_bwa_default.ini
     #else if $configuration.configuration_switch == 'Default for Isaac':
          --configFile				strelka_config_isaac_default.ini
     #else if $configuration.configuration_switch == 'Default for Eland':
          --configFile				strelka_config_eland_default.ini
     #else if $configuration.configuration_switch == 'Path':
          --configFile				$configuration.configFile
     #else:
          --configFile				Custom
          --depthFilterMultiple 			$configuration.depthFilterMultiple
          --snvMaxFilteredBasecallFrac		$configuration.snvMaxFilteredBasecallFrac
          --snvMaxSpanningDeletionFrac 		$configuration.snvMaxSpanningDeletionFrac
          --indelMaxRefRepeat			$configuration.indelMaxRefRepeat
          --indelMaxWindowFilteredBasecallFrac	$configuration.indelMaxWindowFilteredBasecallFrac
          --indelMaxIntHpolLength			$configuration.indelMaxIntHpolLength
          --ssnvPrior				$configuration.ssnvPrior
          --sindelPrior				$configuration.sindelPrior
          --ssnvNoise				$configuration.ssnvNoise
          --sindelNoise				$configuration.sindelNoise
          --ssnvNoiseStrandBiasFrac		$configuration.ssnvNoiseStrandBiasFrac
          --minTier1Mapq				$configuration.minTier1Mapq
          --minTier2Mapq				$configuration.minTier2Mapq
          --ssnvQuality_LowerBound		$configuration.ssnvQuality_LowerBound
          --sindelQuality_LowerBound		$configuration.sindelQuality_LowerBound
          --isWriteRealignedBam			$configuration.isWriteRealignedBam
          --binSize 				$configuration.binSize
          --isSkipDepthFilters			$configuration.isSkipDepthFilters
          --maxInputDepth 			$configuration.maxInputDepth
          #if $configuration.extra_arguments.extra_arguments_switch == 'Yes':
            --extraStrelkaArguments 		yes
            #if $configuration.extra_arguments.a:
              -a
            #end if
            #if $configuration.extra_arguments.b:
              -b $configuration.extra_arguments.barg
            #end if
            #if $configuration.extra_arguments.c:
              -c $configuration.extra_arguments.carg
            #end if
            #if $configuration.extra_arguments.d:
              -d $configuration.extra_arguments.darg
            #end if
            #if $configuration.extra_arguments.e:
              -e $configuration.extra_arguments.earg
            #end if
        #end if
     #end if
          
     </command>
  </macro>
</macros>