Merge branch 'feature-raxml_extension' into 'develop'

Feature raxml extension

See #80

See merge request !31

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

+package nl.lumc.sasc.biopet.extensions
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import java.io.File
+
+class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
+
+  override val defaultThreads = 4
+  override def versionCommand = executable + " -v"
+  override val versionRegex = """.*version \w* .*""".r
+  
+  @Input(doc = "Input phy/fasta file", required = true)
+  var input: File = _
+
+  @Argument(doc = "Model", required = true)
+  var m: String = _
+
+  @Argument(doc = "Parsimony seed", required = false)
+  var p: Option[Int] = config("p")
+
+  @Argument(doc = "Bootstrapping seed", required = false)
+  var b: Option[Int] = config("b")
+
+  @Argument(doc = "Number of runs", required = false)
+  var N: Option[Int] = config("N")
+
+  @Argument(doc = "Name of output files", required = true)
+  var n: String = _
+  
+  @Argument(doc = "Name of output files", required = true)
+  var f: String = "d"
+
+  @Argument(doc = "Output directory", required = false)
+  var w: String = jobLocalDir.getAbsolutePath
+  
+  @Input(required = false)
+  var t: File = _
+  
+  @Input(required = false)
+  var z: File = _
+  
+  @Output(doc = "Output files", required = false)
+  private var out: List[File] = Nil
+  
+  executable = config("exe", default = "raxmlHPC")
+
+  override def afterGraph {
+    super.afterGraph
+    f match {
+      case "d" if b.isEmpty => out +:= getBestTree
+      case "d" if b.isDefined => out +:= getBootstrap
+    }
+  }
+  
+  def getBestTree: File = new File(w + File.separator + "RAxML_bestTree." + n)
+  def getBootstrap: File = new File(w + File.separator + "RAxML_bootstrap." + n)
+  
+  def cmdLine = required(executable) +
+    required("-m", m) +
+    required("-s", input) +
+    optional("-p", p) +
+    optional("-b", b) +
+    optional("-N", N) +
+    optional("-w", w) +
+    optional("-f", f) +
+    optional("-t", t) +
+    optional("-z", z) +
+    (if (threads > 1) required("-T", threads) else "")
+}
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