Added all arg to centrifuge

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala

@@ -26,6 +26,50 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
   @Output(doc = "Output with hits per sequence")
   var report: Option[File] = None
 
+  @Output(required = false)
+  var un: Option[File] = _
+
+  @Output(required = false)
+  var al: Option[File] = _
+
+  @Output(required = false)
+  var unConc: Option[File] = _
+
+  @Output(required = false)
+  var alConc: Option[File] = _
+
+  @Output(required = false)
+  var metFile: Option[File] = _
+
+  // Input args
+  var q: Boolean = config("q", default = false)
+  var qseq: Boolean = config("qseq", default = false)
+  var f: Boolean = config("f", default = false)
+  var r: Boolean = config("r", default = false)
+  var c: Boolean = config("c", default = false)
+  var skip: Option[Int] = config("skip")
+  var upto: Option[Int] = config("upto")
+  var trim5: Option[Int] = config("trim5")
+  var trim3: Option[Int] = config("trim3")
+  var phred33: Boolean = config("phred33", default = false)
+  var phred64: Boolean = config("phred64", default = false)
+  var intQuals: Boolean = config("int_quals", default = false)
+  var ignoreQuals: Boolean = config("ignore_quals", default = false)
+  var nofw: Boolean = config("nofw", default = false)
+  var norc: Boolean = config("norc", default = false)
+
+  // Classification args
+  var minHitlen = Option[Int] = config("min_hitlen")
+  var minTotallen: Option[Int] = config("min_totallen")
+  var hostTaxids: List[Int] = config("host_taxids", default = Nil)
+  var excludeTaxids: List[Int] = config("exclude_taxids", default = Nil)
+
+  // Output args
+  var t: Boolean = config("t", default = false)
+  var quiet: Boolean = config("quiet", default = false)
+  var metStderr: Boolean = config("met_stderr", default = false)
+  var met: Option[Int] = config("met")
+
   override def defaultThreads = 8
 
   executable = config("exe", default = "centrifuge", freeVar = false)
@@ -49,7 +93,34 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
    * @return Command to run
    */
   def cmdLine: String = executable +
-    //TODO: Options
+    conditional(q, "-q") +
+    conditional(qseq, "--qseq") +
+    conditional(f, "-f") +
+    conditional(r, "-r") +
+    conditional(c, "-c") +
+    optional("--skip", skip) +
+    optional("--upto", upto) +
+    optional("--trim5", trim5) +
+    optional("--trim3", trim3) +
+    conditional(phred33, "--phred33") +
+    conditional(phred64, "--phred64") +
+    conditional(intQuals, "--int-quals") +
+    conditional(ignoreQuals, "--ignore-quals") +
+    conditional(nofw, "--nofw") +
+    conditional(norc, "--norc") +
+    optional("--min-hitlen", minHitlen) +
+    optional("--min-totallen", minTotallen) +
+    optional("--host-taxids", if (hostTaxids.nonEmpty) Some(hostTaxids.mkString(",")) else None) +
+    optional("--exclude-taxids", if (excludeTaxids.nonEmpty) Some(excludeTaxids.mkString(",")) else None) +
+    optional("--met-file", metFile) +
+    conditional(t, "-t") +
+    conditional(quiet, "--quiet") +
+    conditional(metStderr, "--met-stderr") +
+    optional("--met", met) +
+    optional(if (un.exists(_.getName.endsWith(".gz"))) "--un-gz" else "--un", un) +
+    optional(if (al.exists(_.getName.endsWith(".gz"))) "--al-gz" else "--al", al) +
+    optional(if (unConc.exists(_.getName.endsWith(".gz"))) "--un-conc-gz" else "--un-conc", unConc) +
+    optional(if (alConc.exists(_.getName.endsWith(".gz"))) "--al-conc-gz" else "--al-conc", alConc) +
     optional("--threads", threads) +
     required("-x", index) +
     (inputR2 match {