Added samse

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

+package nl.lumc.sasc.biopet.extensions.bwa
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 1/16/15.
+ */
+class BwaSamse(val root: Configurable) extends Bwa {
+  @Input(doc = "Fastq file", required = true)
+  var fastq: File = _
+
+  @Input(doc = "Sai file", required = true)
+  var sai: File = _
+
+  @Input(doc = "The reference file for the bam files.", required = true)
+  var reference: File = config("reference", required = true)
+
+  @Output(doc = "Output file SAM", required = false)
+  var output: File = _
+
+  var n: Option[Int] = config("n")
+  var r: String = _
+
+  def cmdLine = required(executable) +
+    required("samse") +
+    optional("-n", n) +
+    optional("-f", output) +
+    optional("-r", r) +
+    required(reference) +
+    required(sai) +
+    required(fastq)
+}