xhmm discover wrapper

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala

+package nl.lumc.sasc.biopet.extensions.xhmm
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
+
+/**
+  * Created by Sander Bollen on 23-11-16.
+  */
+class XhmmDiscover(val root: Configurable) extends Xhmm {
+
+  @Input
+  var inputMatrix: File = _
+
+  @Output
+  var outputXcnv: File = _
+
+  @Input
+  var r: File = _
+
+  @Argument
+  var discoverParamsFile: File = config("discover_params", namespace = "xhmm")
+
+  private lazy val outputXcnvAuxFile: File = {
+    new File(outputXcnv.getAbsolutePath + ".aux")
+  }
+
+  @Argument
+  var xhmmAnalysisName: String = _
+
+  def cmdLine = {
+    executable + required("--discover") +
+      required("-r", inputMatrix) +
+      required("-R", r) +
+      required("-c", outputXcnv) +
+      required("-a", outputXcnvAuxFile) +
+      required("-s", xhmmAnalysisName)
+  }
+
+}