Commit b220a035 authored by Sander Bollen's avatar Sander Bollen

wrapper for xcnv to bed

parent d64c43d1
package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
/**
* Created by Sander Bollen on 24-11-16.
*/
class XcnvToBed(val root: Configurable) extends ToolCommandFunction {
def toolObject = nl.lumc.sasc.biopet.tools.XcnvToBed
@Input
var inputXcnv: File = _
@Output
var outpuBed: File = _
@Argument
var sample: String = _
override def cmdLine = {
super.cmdLine + required("-I", inputXcnv) + required("-O", outpuBed) + required("-S", sample)
}
}
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