Commit d97b0242 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added text to args

parent 37b7f677
......@@ -40,22 +40,22 @@ object VcfToTsv extends ToolCommand {
} text "output file, default to stdout"
opt[String]('f', "field") unbounded () action { (x, c) =>
c.copy(fields = x :: c.fields)
}
} text "Genotype field to use" valueName "Genotype field name"
opt[String]('i', "info_field") unbounded () action { (x, c) =>
c.copy(infoFields = x :: c.infoFields)
}
} text "Info field to use" valueName "Info field name"
opt[Unit]("all_info") unbounded () action { (x, c) =>
c.copy(allInfo = true)
}
} text "Use all info fields in the vcf header"
opt[Unit]("all_format") unbounded () action { (x, c) =>
c.copy(allFormat = true)
}
} text "Use all genotype fields in the vcf header"
opt[String]('s', "sample_field") unbounded () action { (x, c) =>
c.copy(sampleFields = x :: c.sampleFields)
}
} text "Genotype fields to use in the tsv file"
opt[Unit]('d', "disable_defaults") unbounded () action { (x, c) =>
c.copy(disableDefaults = true)
}
} text "Don't output the default columns from the vcf file"
opt[String]("separator") maxOccurs 1 action { (x, c) =>
c.copy(separator = x)
} text "Optional separator. Default is tab-delimited"
......
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