--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/strelka2/strelka2.xml	Thu Sep 25 11:59:08 2014 -0400
@@ -0,0 +1,126 @@
+<tool id="strelka88" name="Strelka good interface but no dependencies">
+
+  <description>Strelka good interface but no dependencies</description>
+  <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
+   </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" label="isWriteRealignedBam" />
+        <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>  
+    <conditional name="conf_file">
+      <param name="conf_file_switch" type="select" label="output conf_file ?">
+        <option value="No" selected="true">No</option>
+        <option value="Yes">Yes</option>
+      </param>
+    </conditional>
+
+
+
+
+  </inputs>
+
+  <outputs>
+    <data format="vcf" name="output1_vcf" label="${tool.name} on ${on_string}(passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf"/>
+    <data format="vcf" name="output2_vcf" label="${tool.name} on ${on_string}(passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf"/>
+    <data format="vcf" name="output3_vcf" label="${tool.name} on ${on_string}(all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf"/>
+    <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf"/>
+    <data name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/tmp/config.ini">
+      <filter>conf_file.conf_file_switch == "Yes"</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>