Commit 6b51387d authored by Sander Bollen's avatar Sander Bollen
Browse files

xhmm normalize wrapper

parent aedc6bcd
package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
/**
* Created by Sander Bollen on 23-11-16.
*/
class XhmmNormalize(val root: Configurable) extends Xhmm {
@Input
var inputMatrix: File = _
@Input
var pcaFile: File = _
@Output
var normalizeOutput: File = _
@Argument
var normalizeMethod: String = config("normalize_method", namespace = "xhmm", default = "PVE_mean")
@Argument
var pveFactor: Float = config("pve_mean_factor", namespace = "xhmm", default = 0.7)
def cmdLine = {
executable + required("--normalize") +
required("-r", inputMatrix) +
required("--PCAfiles", pcaFile) +
required("--normalizeOutput", normalizeOutput) +
required("--PCnormalizeMethod", normalizeMethod) +
required("--PVE_mean_factor", pveFactor)
}
}
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