Added Seqstat wrapper

flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.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 Seqstat(val globalConfig: Config) extends CommandLineFunction with Python {
+  def this() = this(new Config(Map()))
+  analysisName = "seqstat"
+  val config: Config = globalConfig.getAsConfig(analysisName)
+  logger.debug("Config for " + analysisName + ": " + config)
+  
+  setPythonScript("__init__.py", "scripts/pyfastqc/")
+  setPythonScript("seq_stat.py", "scripts/")
+  
+  @Input(doc="Fastq input", shortName="fastqc", required=true) var input_fastq: File = _
+  @Input(doc="Dep", shortName="dep", required=false) var deps: List[File] = Nil
+  @Output(doc="Output file", shortName="out", required=true) var out: File = _
+  
+  var fmt: String = _
+  
+  def commandLine = {
+    getPythonCommand + 
+    optional("--fmt", fmt) + 
+    required("-o", out) + 
+    required(input_fastq)
+  }
+}