Add output arg to sampletsvtojson

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.File
+import java.io.{PrintWriter, File}
 
 import nl.lumc.sasc.biopet.core.ToolCommand
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
@@ -27,12 +27,15 @@ import scala.io.Source
  * This tool can convert a tsv to a json file
  */
 object SamplesTsvToJson extends ToolCommand {
-  case class Args(inputFiles: List[File] = Nil) extends AbstractArgs
+  case class Args(inputFiles: List[File] = Nil, outputFile: Option[File] = None) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('i', "inputFiles") required () unbounded () valueName "<file>" action { (x, c) =>
+    opt[File]('i', "inputFiles") required() unbounded() valueName "<file>" action { (x, c) =>
       c.copy(inputFiles = x :: c.inputFiles)
     } text "Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed"
+    opt[File]('o', "outputFile") unbounded() valueName "<file>" action { (x, c) =>
+      c.copy(outputFile = Some(x))
+    }
   }
 
   /** Executes SamplesTsvToJson */
@@ -41,7 +44,14 @@ object SamplesTsvToJson extends ToolCommand {
     val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
 
     val jsonString = stringFromInputs(commandArgs.inputFiles)
-    println(jsonString)
+    commandArgs.outputFile match {
+      case Some(file) => {
+        val writer = new PrintWriter(file)
+        writer.println(jsonString)
+        writer.close()
+      }
+      case _ => println(jsonString)
+    }
   }
 
   def mapFromFile(inputFile: File): Map[String, Any] = {