Adding extensions for stringtie

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/Stringtie.scala

+package nl.lumc.sasc.biopet.extensions.stringtie
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+import scala.util.matching.Regex
+
+class Stringtie(val parent: Configurable)
+  extends BiopetCommandLineFunction
+    with Reference
+    with Version {
+
+  executable = config("exe", "stringtie")
+
+  @Input(required = true)
+  var inputBam: File = _
+
+  @Output
+  var outputGtf: File = _
+
+  @Output
+  var geneAbundances: Option[File] = None
+
+  @Output
+  var referenceCoverage: Option[File] = None
+
+  var rf: Boolean = config("rf", default = false)
+  var fr: Boolean = config("fr", default = false)
+
+  var v: Boolean = config("v", default = logger.isDebugEnabled)
+  var l: Option[String] = None
+  var f: Option[Double] = config("f")
+  var m: Option[Int] = config("m")
+  var a: Option[Int] = config("a")
+  var j: Option[Float] = config("j")
+  var t: Boolean = config("t", default = false)
+  var c: Option[Float] = config("c")
+  var g: Option[Int] = config("g")
+  var B: Boolean = config("B", default = false)
+  var b: Option[String] = config("b")
+  var e: Boolean = config("e", default = false)
+  var M: Option[Float] = config("M")
+  var x: List[String] = config("x", default = Nil)
+
+  /** Command to get version of executable */
+  def versionCommand: String = executable + " --version"
+
+  /** Regex to get version from version command output */
+  def versionRegex: Regex = ".*".r
+
+  def cmdLine: String = required(executable) +
+    conditional(v, "-v") +
+    required("-p", threads) +
+    conditional(rf, "--rf") +
+    conditional(fr, "--fr") +
+    optional("-l", l) +
+    optional("-f", f) +
+    optional("-m", m) +
+    optional("-A", geneAbundances) +
+    optional("-C", referenceCoverage) +
+    optional("-a", a) +
+    optional("-j", j) +
+    conditional(t, "-t") +
+    optional("-c", c) +
+    optional("-g", g) +
+    conditional(B, "-B") +
+    optional("-b", b) +
+    conditional(e, "-e") +
+    optional("-M", M) +
+    (if (x.nonEmpty) optional("-x", x.mkString(",")) else "") +
+    (if (outputAsStdout) "" else required("-o", outputGtf))
+
+}

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/StringtieMerge.scala

+package nl.lumc.sasc.biopet.extensions.stringtie
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+import scala.util.matching.Regex
+
+class StringtieMerge(val parent: Configurable)
+  extends BiopetCommandLineFunction
+      with Reference
+      with Version {
+
+    executable = config("exe", "stringtie")
+
+    @Input(required = true)
+    var inputBam: File = _
+
+    @Output
+    var outputGtf: File = _
+
+
+    var v: Boolean = config("v", default = logger.isDebugEnabled)
+    var l: Option[String] = None
+    var f: Option[Double] = config("f")
+    var m: Option[Int] = config("m")
+    var c: Option[Float] = config("c")
+    var F: Option[Double] = config("F")
+    var T: Option[Double] = config("T")
+    var i: Boolean = config("i", default = false)
+
+    /** Command to get version of executable */
+    def versionCommand: String = executable + " --version"
+
+    /** Regex to get version from version command output */
+    def versionRegex: Regex = ".*".r
+
+    def cmdLine: String = required(executable) +
+      conditional(v, "-v") +
+      required("-p", threads) +
+      optional("-l", l) +
+      optional("-f", f) +
+      optional("-m", m) +
+      optional("-c", c) +
+      optional("-F", F) +
+      conditional(i, "-i") +
+      (if (outputAsStdout) "" else required("-o", outputGtf))
+
+  }