Commit e34fe3a1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding a simple placeholder for a tool

parent d36878da
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)
}
}
......@@ -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>
......
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