Adding tophat

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

+package nl.lumc.sasc.biopet.extensions.aligners
+
+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 TopHat(val root: Configurable) extends BiopetCommandLineFunction {
+  @Input(doc = "FastQ file R1", shortName = "R1")
+  var R1: File = _
+
+  @Input(doc = "FastQ file R2", shortName = "R2", required = false)
+  var R2: File = _
+
+  @Input(doc = "Bowtie index", shortName = "bti")
+  var bowtie_index: File = config("bowtie_index", required = true)
+
+  @Argument(doc = "Output Directory")
+  var outputDir: String = _
+
+  @Output(doc = "Output file SAM", shortName = "output")
+  var output: File = _
+
+  // options set via API or config
+  //  var numrecords: String = config("numrecords", default = "all")
+  //  var solexa: Boolean = config("solexa", default = false)
+  //  var solexaold: Boolean = config("solexaold", default = false)
+  //  var sanger: Boolean = config("sanger", default = false)
+  //
+  //  var insertsize: Option[Int] = config("insertsize", default = 250)
+  //  var insertsd: Option[Int] = config("insertsd", default = 60)
+  //  var insertsize2: Option[Int] = config("insertsize2", default = -2000)
+  //  var insertsd2: Option[Int] = config("insertsd2", default = -1)
+  //
+  //  var sensitive: Boolean = config("sensitive", default = false)
+  //  var fast: Boolean = config("fast", default = false)
+  //
+  //  var readgroup: String = config("readgroup")
+  //  var verbosity: Option[Int] = config("verbosity", default = 2)
+  //  var logfile: String = config("logfile")
+
+  executable = config("exe", default = "tophat", freeVar = false)
+  override val versionRegex = """TopHat v(.*)""".r
+  override val versionExitcode = List(0, 1)
+
+  override val defaultVmem = "4G"
+  override val defaultThreads = 8
+
+  override def versionCommand = executable + " --version"
+
+  override def afterGraph() {
+    if (!outputDir.endsWith("/")) outputDir += "/"
+    output = new File(outputDir + "accepted_hits.bam")
+  }
+
+  def cmdLine: String = {
+    var cmd: String = required(executable) +
+      optional("-p", nCoresRequest) +
+      "--no-convert-bam" +
+      required(bowtie_index) +
+      required(R1) + optional(R2)
+    return cmd
+  }
+}