Fix tool extensions

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala

@@ -6,5 +6,12 @@ import nl.lumc.sasc.biopet.FullVersion
  * Created by pjvanthof on 11/09/15.
  */
 trait ToolCommandFuntion extends BiopetJavaCommandLineFunction {
+  def toolObject: Object
+
   override def getVersion = Some("Biopet " + FullVersion)
+
+  override def freezeFieldValues(): Unit = {
+    javaMainClass = toolObject.getClass.getName.split("$").head
+    super.freezeFieldValues()
+  }
 }

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

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
-  javaMainClass = nl.lumc.sasc.biopet.tools.BastyGenerateFasta.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.BastyGenerateFasta
 
   @Input(doc = "Input vcf file", required = false)
   var inputVcf: File = _

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

@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * @deprecated Use picard.util.BedToIntervalList instead
  */
 class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.BedToInterval.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.BedToInterval
 
   @Input(doc = "Input Bed file", required = true)
   var input: File = _

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

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts
 
   @Input(doc = "Input fasta", shortName = "input", required = true)
   var input: File = _

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

@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
-  javaMainClass = nl.lumc.sasc.biopet.tools.BiopetFlagstat.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.BiopetFlagstat
 
   @Input(doc = "Input bam", shortName = "input", required = true)
   var input: File = _

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

@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * @param root Parent object
  */
 class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.FastqSplitter.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.FastqSplitter
 
   @Input(doc = "Input fastq", shortName = "input", required = true)
   var input: File = _

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

@@ -32,7 +32,7 @@ import scala.util.matching.Regex
  */
 class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summarizable {
 
-  javaMainClass = nl.lumc.sasc.biopet.tools.FastqSync.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.FastqSync
 
   @Input(doc = "Original FASTQ file (read 1 or 2)", shortName = "r", required = true)
   var refFastq: File = null

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

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.MergeAlleles.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.MergeAlleles
 
   @Input(doc = "Input vcf files", shortName = "input", required = true)
   var input: List[File] = Nil

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

@@ -30,7 +30,7 @@ import scala.collection.mutable.{ Set => MutSet }
  */
 class MergeTables(val root: Configurable) extends ToolCommandFuntion {
 
-  javaMainClass = nl.lumc.sasc.biopet.tools.MergeTables.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.MergeTables
 
   override def defaultCoreMemory = 6.0
 

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

@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.collection.JavaConversions._
 
 class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
-  javaMainClass = nl.lumc.sasc.biopet.tools.MpileupToVcf.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.MpileupToVcf
 
   @Input(doc = "Input mpileup file", shortName = "mpileup", required = false)
   var inputMpileup: File = _

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

@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
  * Created by pjvan_thof on 1/13/15.
  */
 class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.PrefixFastq.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.PrefixFastq
 
   override def defaultCoreMemory = 1.0
 

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

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SageCountFastq.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SageCountFastq
 
   @Input(doc = "Input fasta", shortName = "input", required = true)
   var input: File = _

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

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SageCreateLibrary.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SageCreateLibrary
 
   @Input(doc = "Input fasta", shortName = "input", required = true)
   var input: File = _

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

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SageCreateTagCounts.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SageCreateTagCounts
 
   @Input(doc = "Raw count file", shortName = "input", required = true)
   var input: File = _

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

@@ -14,7 +14,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
  * @param root Configuration object for the pipeline
  */
 class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SeqStat.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SeqStat
 
   @Input(doc = "Input FASTQ", shortName = "input", required = true)
   var input: File = null

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

@@ -10,7 +10,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * Created by pjvanthof on 22/08/15.
  */
 class SquishBed(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SquishBed.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SquishBed
 
   @Input(doc = "Input Bed file", required = true)
   var input: File = _

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

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.VcfFilter.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.VcfFilter
 
   @Input(doc = "Input vcf", shortName = "I", required = true)
   var inputVcf: File = _

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

@@ -30,7 +30,7 @@ import scala.io.Source
  * Created by pjvan_thof on 1/10/15.
  */
 class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable with Reference {
-  javaMainClass = nl.lumc.sasc.biopet.tools.VcfStats.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.VcfStats
 
   @Input(doc = "Input fastq", shortName = "I", required = true)
   var input: File = _

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

@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * Biopet extension for tool VcfWithVcf
  */
 class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.VcfWithVcf.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.VcfWithVcf
 
   @Input(doc = "Input vcf file", shortName = "input", required = true)
   var input: File = _

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

@@ -32,7 +32,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  */
 
 class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.VepNormalizer.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.VepNormalizer
 
   @Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
   var inputVCF: File = null