xhmm normalize wrapper

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.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 XhmmNormalize(val root: Configurable) extends Xhmm {
+
+  @Input
+  var inputMatrix: File = _
+
+  @Input
+  var pcaFile: File = _
+
+  @Output
+  var normalizeOutput: File = _
+
+  @Argument
+  var normalizeMethod: String = config("normalize_method", namespace = "xhmm", default = "PVE_mean")
+
+  @Argument
+  var pveFactor: Float = config("pve_mean_factor", namespace = "xhmm", default = 0.7)
+
+  def cmdLine = {
+    executable + required("--normalize") +
+      required("-r", inputMatrix) +
+      required("--PCAfiles", pcaFile) +
+      required("--normalizeOutput", normalizeOutput) +
+      required("--PCnormalizeMethod", normalizeMethod) +
+      required("--PVE_mean_factor", pveFactor)
+  }
+
+}