Added Summarize flexiprep wrapper

flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala

+package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
+
+import nl.lumc.sasc.biopet.core._
+import org.broadinstitute.sting.queue.function.CommandLineFunction
+import nl.lumc.sasc.biopet.wrappers.Python
+import org.broadinstitute.sting.commandline._
+import java.io.File
+
+class Summarize(val globalConfig: Config) extends CommandLineFunction with Python {
+  def this() = this(new Config(Map()))
+  analysisName = "flexiprep_sumarize"
+  val config: Config = globalConfig.getAsConfig(analysisName)
+  logger.debug("Config for " + analysisName + ": " + config)
+  
+  setPythonScript("__init__.py", "scripts/pyfastqc/")
+  setPythonScript("summarize_flexiprep.py", "scripts/")
+  
+  @Input(doc="Dep", shortName="dep", required=false) var deps: List[File] = Nil
+  @Output(doc="Output file", shortName="out", required=true) var out: File = _
+  
+  var samplea: String = _
+  var sampleb: String = _
+  var runDir: String = _
+  var samplename: String = _
+  var trim: Boolean = true
+  var clip: Boolean = true
+  
+  def commandLine = {
+    var mode: String = ""
+    if (clip) mode += "clip"
+    if (trim) mode += "trim"
+    if (mode.isEmpty) mode = "none"
+    
+    getPythonCommand + 
+    optional("--run-dir", runDir) +
+    optional("--sampleb", sampleb) +
+    required(samplename) + 
+    required(mode) + 
+    required(samplea) + 
+    required(out)
+  }
+}
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