Added extension for gubbins script

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+
+class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
+
+  @Input(doc = "Contaminants", required = false)
+  var startingTree: File = config("starting_tree")
+
+  @Input(doc = "Fasta file", shortName = "FQ")
+  var fastafile: File = _
+
+  @Output(doc = "Output", shortName = "out")
+  var outputFiles: List[File] = Nil
+
+  @Argument(required = true)
+  var outputDirectory: String = _
+
+  executable = config("exe", default = "run_gubbins.py")
+  var outgroup: String = config("outgroup")
+  var filterPercentage: String = config("filter_percentage")
+  var treeBuilder: String = config("tree_builder")
+  var iterations: Option[Int] = config("iterations")
+  var minSnps: Option[Int] = config("min_snps")
+  var convergeMethod: String = config("converge_method")
+  var useTimeStamp: Boolean = config("use_time_stamp")
+  var prefix: String = config("prefix")
+  var verbose: Boolean = config("verbose")
+  var noCleanup: Boolean = config("no_cleanup")
+
+  override def afterGraph: Unit = {
+    super.afterGraph
+    if (prefix == null) prefix = fastafile.getName
+    val out: List[String] = List(".recombination_predictions.embl",
+      ".recombination_predictions.gff",
+      ".branch_base_reconstruction.embl",
+      ".summary_of_snp_distribution.vcf",
+      ".per_branch_statistics.csv",
+      ".filtered_polymorphic_sites.fasta",
+      ".filtered_polymorphic_sites.phylip",
+      ".final_tree.tre")
+    for (t <- out) outputFiles ::= new File(outputDirectory + File.separator + prefix + t)
+  }
+
+  def cmdLine = required(executable) +
+    optional("--outgroup", outgroup) +
+    optional("--starting_tree", startingTree) +
+    optional("--filter_percentage", filterPercentage) +
+    optional("--tree_builder", treeBuilder) +
+    optional("--iterations", iterations) +
+    optional("--min_snps", minSnps) +
+    optional("--converge_method", convergeMethod) +
+    conditional(useTimeStamp, "--use_time_stamp") +
+    optional("--prefix", prefix) +
+    conditional(verbose, "--verbose") +
+    conditional(noCleanup, "--no_cleanup") +
+    required(fastafile)
+}