Added PickRepSet

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala

@@ -2,14 +2,14 @@ package nl.lumc.sasc.biopet.extensions.qiime
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
 
 /**
  * Created by pjvan_thof on 12/4/15.
  */
-class PickOtus(val root: Configurable) extends BiopetCommandLineFunction {
+class PickOtus(val root: Configurable) extends BiopetCommandLineFunction with Version {
   executable = config("exe", default = "pick_otus.py")
 
   @Input(required = true)
@@ -18,8 +18,9 @@ class PickOtus(val root: Configurable) extends BiopetCommandLineFunction {
   var outputDir: File = null
 
   override def defaultThreads = 2
-
   override def defaultCoreMemory = 5.0
+  def versionCommand = executable + " --version"
+  def versionRegex = """Version: (.*)""".r
 
   var otu_picking_method: Option[String] = config("otu_picking_method")
   var clustering_algorithm: Option[String] = config("clustering_algorithm")
@@ -76,6 +77,19 @@ class PickOtus(val root: Configurable) extends BiopetCommandLineFunction {
   var usearch61_sort_method: Option[String] = config("usearch61_sort_method")
   var sizeorder: Boolean = config("sizeorder", default = false)
 
+  private lazy val name = inputFasta.getName.stripSuffix(".fasta").stripSuffix(".fa").stripSuffix(".fna")
+
+  def clustersFile = new File(outputDir, s"${name}_clusters.uc")
+  def logFile = new File(outputDir, s"${name}_otus.log")
+  def otusTxt = new File(outputDir, s"${name}_otus.txt")
+
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    outputFiles :+= clustersFile
+    outputFiles :+= logFile
+    outputFiles :+= otusTxt
+  }
+
   def cmdLine = executable +
     required("-i", inputFasta) +
     required("-o", outputDir) +

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala

+package nl.lumc.sasc.biopet.extensions.qiime
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 12/4/15.
+ */
+class PickRepSet(val root: Configurable) extends BiopetCommandLineFunction with Version {
+  executable = config("exe", default = "pick_rep_set.py")
+
+  @Input(required = true)
+  var inputFile: File = _
+
+  @Output
+  var outputFasta: Option[File] = None
+
+  @Output
+  var logFile: Option[File] = None
+
+  @Input(required = false)
+  var reference_seqs_fp: Option[File] = config("reference_seqs_fp")
+
+  var outputDir: File = _
+  var sortBy: Option[String] = config("sort_by")
+
+  def versionCommand = executable + " --version"
+  def versionRegex = """Version: (.*)""".r
+
+  var rep_set_picking_method: Option[String] = config("rep_set_picking_method")
+
+  def cmdLine = executable +
+    required("-i", inputFile) +
+    optional("-f", outputFasta) +
+    optional("-m", rep_set_picking_method) +
+    required("-o", outputDir) +
+    optional("-l", logFile) +
+    optional("-s", sortBy) +
+    optional("-r", reference_seqs_fp)
+}

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRatx.scala

 package nl.lumc.sasc.biopet.pipelines.gears
 
 import nl.lumc.sasc.biopet.core.BiopetQScript
-import nl.lumc.sasc.biopet.extensions.qiime.PickOtus
+import nl.lumc.sasc.biopet.extensions.qiime.{ PickRepSet, PickOtus }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -23,5 +23,13 @@ class GearsQiimeRatx(val root: Configurable) extends QScript with BiopetQScript
     pickOtus.inputFasta = fastaR1
     pickOtus.outputDir = new File(outputDir, "pick_otus")
     add(pickOtus)
+
+    val pickRepSet = new PickRepSet(this)
+    pickRepSet.outputDir = new File(outputDir, "pick_rep_set")
+    pickRepSet.inputFile = pickOtus.otusTxt
+    pickRepSet.outputFasta = Some(new File(pickRepSet.outputDir, fastaR1.getName))
+    pickRepSet.logFile = Some(new File(pickRepSet.outputDir, fastaR1.getName
+      .stripSuffix(".fasta").stripSuffix(".fa").stripSuffix(".fna") + ".log"))
+    add(pickRepSet)
   }
 }