merge comments on xhmm wrappers

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

 package nl.lumc.sasc.biopet.extensions.xhmm
 
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 
 /**
  * Created by Sander Bollen on 23-11-16.
@@ -10,6 +12,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
 abstract class Xhmm extends BiopetCommandLineFunction with Version {
 
   executable = config("exe", namespace = "xhmm", default = "xhmm")
+  var discoverParamsFile: File = config("discover_params", namespace = "xhmm")
 
   def versionCommand = executable + " --version"
   def versionRegex = """xhmm (.*)""".r

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

@@ -22,16 +22,21 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
   @Input
   var r: File = _
 
-  @Argument
-  var discoverParamsFile: File = config("discover_params", namespace = "xhmm")
+  private var _outputXcnvAuxFile: File = _
 
-  private lazy val outputXcnvAuxFile: File = {
-    new File(outputXcnv.getAbsolutePath + ".aux")
-  }
+  @Output
+  var outputXcnvAuxFile = _outputXcnvAuxFile
 
-  @Argument
   var xhmmAnalysisName: String = _
 
+  override def beforeGraph() = {
+    super.beforeGraph()
+    if (outputXcnv == null) {
+      throw new IllegalStateException("Must set output file")
+    }
+    _outputXcnvAuxFile = new File(outputXcnv.getAbsolutePath + ".aux")
+  }
+
   def cmdLine = {
     executable + required("--discover") +
       required("-r", inputMatrix) +

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

@@ -23,8 +23,15 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
   @Input
   var r: File = _
 
-  @Argument
-  var discoverParamsFile: File = config("discover_params", namespace = "xhmm")
+  @Input
+  var f: File = _
+
+  override def beforeGraph() = {
+    super.beforeGraph()
+    if (f == null) {
+      f = referenceFasta()
+    }
+  }
 
   def cmdLine = {
     executable + required("--genotype") +
@@ -32,7 +39,7 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
       required("-r", inputMatrix) +
       required("-R", r) +
       required("-g", inputXcnv) +
-      required("-F", referenceFasta()) +
+      required("-F", f) +
       required("-v", outputVcf)
   }
 

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

@@ -28,37 +28,26 @@ class XhmmMatrix(val root: Configurable) extends Xhmm {
   @Input(required = false)
   var inputExcludeSamples: List[File] = Nil
 
-  @Argument
-  var minTargetSize: Int = config("min_target_size", namespace = "xhmm", default = 10)
+  var minTargetSize: Int = config("min_target_size", namespace = "xhmm_matrix", default = 10)
 
-  @Argument
-  var maxTargetSize: Int = config("max_target_size", namespace = "xhmm", default = 10000)
+  var maxTargetSize: Int = config("max_target_size", namespace = "xhmm_matrix", default = 10000)
 
-  @Argument
-  var minMeanTargetRD: Int = config("min_mean_target_rd", namespace = "xhmm", default = 10)
+  var minMeanTargetRD: Int = config("min_mean_target_rd", namespace = "xhmm_matrix", default = 10)
 
-  @Argument
-  var maxMeanTargetRD: Int = config("max_mean_target_rd", namespace = "xhmm", default = 500)
+  var maxMeanTargetRD: Int = config("max_mean_target_rd", namespace = "xhmm_matrix", default = 500)
 
-  @Argument
-  var minMeanSampleRD: Int = config("min_mean_sample_rd", namespace = "xhmm", default = 25)
+  var minMeanSampleRD: Int = config("min_mean_sample_rd", namespace = "xhmm_matrix", default = 25)
 
-  @Argument
-  var maxMeanSampleRD: Int = config("max_mean_sample_rd", namespace = "xhmm", default = 200)
+  var maxMeanSampleRD: Int = config("max_mean_sample_rd", namespace = "xhmm_matrix", default = 200)
 
-  @Argument
-  var maxSdSampleRD: Int = config("max_sd_sample_rd", namespace = "xhmm", default = 150)
+  var maxSdSampleRD: Int = config("max_sd_sample_rd", namespace = "xhmm_matrix", default = 150)
 
-  @Argument
-  var maxsdTargetRD: Int = config("max_sd_target_rd", namespace = "xhmm", default = 30)
+  var maxsdTargetRD: Int = config("max_sd_target_rd", namespace = "xhmm_matrix", default = 30)
 
-  @Argument
   var centerData: Boolean = false
 
-  @Argument
   var centerType: String = "sample"
 
-  @Argument
   var zScoreData: Boolean = false
 
   private def subCmdLine = {

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

@@ -17,7 +17,9 @@ class XhmmMergeGatkDepths(val root: Configurable) extends Xhmm {
   var output: File = _
 
   def cmdLine = {
-    executable + required("--mergeGATKdepths") + repeat("--GATKdepths", gatkDepthsFiles) + required("-o", output)
+    executable + required("--mergeGATKdepths") +
+      repeat("--GATKdepths", gatkDepthsFiles) +
+      required("-o", output)
   }
 
 }

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

@@ -19,11 +19,9 @@ class XhmmNormalize(val root: Configurable) extends Xhmm {
   @Output
   var normalizeOutput: File = _
 
-  @Argument
-  var normalizeMethod: String = config("normalize_method", namespace = "xhmm", default = "PVE_mean")
+  var normalizeMethod: String = config("normalize_method", namespace = "xhmm_normalize", default = "PVE_mean")
 
-  @Argument
-  var pveFactor: Float = config("pve_mean_factor", namespace = "xhmm", default = 0.7)
+  var pveFactor: Float = config("pve_mean_factor", namespace = "xhmm_normalize", default = 0.7)
 
   def cmdLine = {
     executable + required("--normalize") +