wrapper for xcnv to bed

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala

+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
+
+/**
+  * Created by Sander Bollen on 24-11-16.
+  */
+class XcnvToBed(val root: Configurable) extends ToolCommandFunction {
+  def toolObject = nl.lumc.sasc.biopet.tools.XcnvToBed
+
+  @Input
+  var inputXcnv: File = _
+
+  @Output
+  var outpuBed: File = _
+
+  @Argument
+  var sample: String = _
+
+  override def cmdLine = {
+    super.cmdLine + required("-I", inputXcnv) + required("-O", outpuBed) + required("-S", sample)
+  }
+
+}