diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala new file mode 100644 index 0000000000000000000000000000000000000000..c42f2ced1f5776c88131c1b466c7b162d7c875b1 --- /dev/null +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala @@ -0,0 +1,37 @@ +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) +} \ No newline at end of file