Commit b7ace90c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added wigToBigWig extension

parent c2fb1f5b
package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 1/29/15.
*/
class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input wig file")
var inputWigFile: File = _
@Input(doc = "Input chrom sizes file")
var inputChromSizesFile: File = _
@Output(doc = "Output BigWig file")
var outputBigWig: File = _
executable = config("exe", default = "wigToBigWig")
var blockSize: Option[Int] = config("blockSize")
var itemsPerSlot: Option[Int] = config("itemsPerSlot")
var clip: Boolean = config("clip", default = false)
var unc: Boolean = config("unc", default = false)
def cmdLine = required(executable) +
optional("blockSize=", blockSize, spaceSeparated = false) +
optional("itemsPerSlot=", itemsPerSlot, spaceSeparated = false) +
conditional(clip, "-clip") +
conditional(unc, "-unc") +
required(inputWigFile) +
required(inputChromSizesFile) +
required(outputBigWig)
}
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