Adding a simple placeholder for a tool

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/JsonToHdf5.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+
+import ncsa.hdf.`object`.h5.H5File
+import nl.lumc.sasc.biopet.tools.GvcfToBed.Args
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand}
+
+/**
+  * Created by pjvanthof on 26/01/2017.
+  */
+object JsonToHdf5 extends ToolCommand {
+
+  case class Args(inputJson: File = null,
+                  outputHdf5: File = null) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('I', "inputJson") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(inputJson = x)
+    } text "Input json file"
+    opt[File]('o', "outputHdf5") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(outputHdf5 = x)
+    } text "Output hdf5 file"
+  }
+
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+
+    val jsonMap = ConfigUtils.fileToConfigMap(cmdArgs.inputJson)
+
+    val hdf5 = new H5File(cmdArgs.outputHdf5.getAbsolutePath)
+
+  }
+
+}

biopet-utils/pom.xml

@@ -30,6 +30,11 @@
     <packaging>jar</packaging>
 
     <dependencies>
+        <dependency>
+            <groupId>org.hdfgroup</groupId>
+            <artifactId>hdf-java</artifactId>
+            <version>2.6.1</version>
+        </dependency>
         <dependency>
             <groupId>colt</groupId>
             <artifactId>colt</artifactId>