<tool id="strelka" name="Strelka">
  <!-- Made by Gregoire Seguin-Henry for geviteam in 2014 -->
  <description>Strelka</description>
  <requirements>
    <requirement type="set_environment">SCRIPT_PATH</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 --refFile $refFile
   #if $configuration.configuration_switch == 'Default':
	--configFile 				Default
   #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 		    $configuration.extra_arguments.extraStrelkaArguments
        #end if
   #end if
        --scriptPath				\$SCRIPT_PATH
   </command>

   <inputs>
    <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
    <param format="bam" name="normalBam" type="data" label="Normal bam file"/>
    <param format="fasta" name="refFile" type="data" label="ref fasta file"/>

    <conditional name="configuration">
      <param name="configuration_switch" type="select" label="how do you want to configure strelka">
        <option value="Default" selected="true">Default</option>
	<option value="Path">Use a config file</option>
        <option value="Custom">Custom</option>
      </param>
      <when value="Default">
        <!-- do nothing -->
      </when>
      <when value="Path">
        <param format="ini" name="configFile" type="data" label="config file"/>
      </when>
      <when value="Custom">
        <param name="binSize" type="integer" value="25000000" label="binSize" />
        <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40" label="minTier1Mapq" />
        <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5" label="minTier2Mapq" />
        <param name="isWriteRealignedBam" type="integer" value="0" min="0" max="1" label="isWriteRealignedBam" help="0 for no alignment else 1"/>
        <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" />
        <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" />
        <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" />
        <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" />
        <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" />
        <param name="ssnvQuality_LowerBound" type="integer" value="15" label="ssnvQuality_LowerBound" />
        <param name="sindelQuality_LowerBound" type="integer" value="30" label="sindelQuality_LowerBound" />
        <param name="isSkipDepthFilters" type="integer" value="1" label="isSkipDepthFilters" />
        <param name="depthFilterMultiple" type="float" value="3.0" label="depthFilterMultiple" />
        <param name="snvMaxFilteredBasecallFrac" type="float" value="0.4" label="snvMaxFilteredBasecallFrac" />
        <param name="snvMaxSpanningDeletionFrac" type="float" value="0.75" label="snvMaxSpanningDeletionFrac" />
        <param name="indelMaxRefRepeat" type="integer" value="8" label="indelMaxRefRepeat" />
        <param name="indelMaxWindowFilteredBasecallFrac" type="float" value="0.3" label="indelMaxWindowFilteredBasecallFrac" />
        <param name="indelMaxIntHpolLength" type="integer" value="14" label="indelMaxIntHpolLength" />
        <param name="maxInputDepth" type="integer" value="10000" label="maxInputDepth" />
        <conditional name="extra_arguments">
	  <param name="extra_arguments_switch" type="select" label="Do you Want to add extraStrelkaArguments?">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
          </param>
          <when value="No">
            <!-- do nothing -->
          </when>
          <when value="Yes"> 
	    <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" />
          </when>
        </conditional>
      </when>
    </conditional>  
      <param name="conf_file_check" type="boolean" label="output conf file" checked="False"/>
      <param name="output1_file_check" type="boolean" label="output passed snvs(filtred)" checked="True"/>     
      <param name="output2_file_check" type="boolean" label="output passed indels(filtred)" checked="True"/>
      <param name="output3_file_check" type="boolean" label="output all snvs" checked="True"/>
      <param name="output4_file_check" type="boolean" label="output all indels" checked="True"/>
      <param name="output5_file_check" type="boolean" label="normal realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/>
      <param name="output6_file_check" type="boolean" label="tumor realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/>

  </inputs>

  <outputs>
    <data format="vcf" name="output1_vcf" label="${tool.name} on ${on_string}(passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf">
      <filter>output1_file_check == True</filter>
    </data>
    <data format="vcf" name="output2_vcf" label="${tool.name} on ${on_string}(passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf">
      <filter>output2_file_check == True</filter>
    </data>
    <data format="vcf" name="output3_vcf" label="${tool.name} on ${on_string}(all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf">
      <filter>output3_file_check == True</filter>
    </data>
    <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf">
      <filter>output4_file_check == True</filter>
    </data>
    <data name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/tmp/config.ini">
      <filter>conf_file_check == True</filter>
    </data>
    <data format="bam" name="output5_bam" label="${tool.name} on ${on_string}(normal.realigned.bam)" from_work_dir="StrelkaAnalysis/realigned/normal.realigned.bam">
      <filter>output5_file_check == True</filter>
    </data>
    <data format="bam" name="output6_bam" label="${tool.name} on ${on_string}(tumor.realigned.bam)" from_work_dir="StrelkaAnalysis/realigned/tumor.realigned.bam">
      <filter>output6_file_check == True</filter>
    </data>
  </outputs>

  <tests>
    <test>
      <param name="normalBam" ftype="bam" value="NA12891_dupmark_chr20_region.bam"/>
      <param name="tumorBam" ftype="bam" value="NA12892_dupmark_chr20_region.bam"/>
      <param name="refFile" ftype="fasta" value="chr20_860k_only.fa"/>
      <param name="configuration_switch" value="Default"/>
      <output name="output1_vcf" file="passed.somatic.snvs.vcf"/>
      <output name="output2_vcf" file="passed.somatic.indels.vcf"/>
      <output name="output3_vcf" file="all.somatic.snvs.vcf"/>
      <output name="output4_vcf" file="all.somatic.indels.vcf"/>
    </test>
  </tests>

  <help>
Strelka, a method for somatic SNV and small indel detectipon from sequencing data of matched tumor-normal samples.
  </help>

</tool>