From acd850186033717372f8b0cd9b55cd7011c049cd Mon Sep 17 00:00:00 2001
From: Ioannis Moustakas <i.moustakas@lumc.nl>
Date: Tue, 5 Jul 2016 15:29:51 +0200
Subject: [PATCH] Improve user documentation for the tool
---
.../lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
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 4478b9f0e..c04622668 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'"
}
/**
--
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