From d97b024281c2cf9f69467c9472b7101662cd2bcb Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 19 Jul 2016 14:36:56 +0200
Subject: [PATCH] Added text to args
---
.../scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
index 1c40d228d..3597d398c 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
@@ -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"
--
GitLab