Commit 250e63be authored by pjvan_thof's avatar pjvan_thof
Browse files

Fixing arguments

parent c913b602
......@@ -31,16 +31,16 @@ object ValidateAnnotation extends ToolCommand {
gtfFiles: List[File] = Nil)
class OptParser extends AbstractOptParser[Args](commandName) {
opt[File]('r', "refflatFile") maxOccurs 1 valueName "<file>" action { (x, c) =>
opt[File]('r', "refflatFile") unbounded() maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(refflatFile = Some(x))
} text "Refflat file to check"
opt[File]('g', "gtfFile") valueName "<file>" action { (x, c) =>
opt[File]('g', "gtfFile") unbounded() valueName "<file>" action { (x, c) =>
c.copy(gtfFiles = x :: c.gtfFiles)
} text "Gtf files to check"
opt[File]('R', "reference") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
opt[File]('R', "reference") unbounded() required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(reference = x)
} text "Reference fasta to check vcf file against"
opt[Unit]("disableFail") maxOccurs 1 valueName "<file>" action { (_, c) =>
opt[Unit]("disableFail") unbounded() maxOccurs 1 valueName "<file>" action { (_, c) =>
c.copy(failOnError = false)
} text "Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0"
}
......
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