diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala index 4478b9f0ef2be289c6836f51e0ea87eff37c7816..c046226689d19262323650ec63925420dcac20b2 100644 --- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala +++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala @@ -52,22 +52,22 @@ object AnnotateVcfWithBed extends ToolCommand { class OptParser extends AbstractOptParser { opt[File]('I', "inputFile") required () unbounded () valueName "<vcf file>" action { (x, c) => c.copy(inputFile = x) - } text "Input is a required file property" + } text "Input VCF file. Mandatory field" opt[File]('B', "bedFile") required () unbounded () valueName "<bed file>" action { (x, c) => c.copy(bedFile = x) - } text "Bedfile is a required file property" + } text "Input Bed file. Mandatory field" opt[File]('o', "output") required () unbounded () valueName "<vcf file>" action { (x, c) => c.copy(outputFile = x) - } text "out is a required file property" + } text "Output VCF file. Mandatory field" opt[String]('f', "fieldName") required () unbounded () valueName "<name of field in vcf file>" action { (x, c) => c.copy(fieldName = x) } text "Name of info field in new vcf file" - opt[String]('d', "fieldDescription") unbounded () valueName "<name of field in vcf file>" action { (x, c) => + opt[String]('d', "fieldDescription") unbounded () valueName "<description of field in vcf file>" action { (x, c) => c.copy(fieldDescription = x) } text "Description of field in new vcf file" - opt[String]('t', "fieldType") unbounded () valueName "<name of field in vcf file>" action { (x, c) => + opt[String]('t', "fieldType") unbounded () valueName "<type of field in vcf file>" action { (x, c) => c.copy(fieldType = x) - } text "Description of field in new vcf file" + } text "Type of field in new vcf file. Can be 'Integer', 'Flag', 'Character', 'Float'" } /**