From 1261f8848b2640064ae9cc0eb6fa925bf7c70fa2 Mon Sep 17 00:00:00 2001
From: Ioannis Moustakas <i.moustakas@lumc.nl>
Date: Wed, 6 Jul 2016 17:07:58 +0200
Subject: [PATCH] Added text in the options parser
---
.../main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
index 8d3f7a0df..014718a9b 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
@@ -38,13 +38,13 @@ object BaseCounter extends ToolCommand {
class OptParser extends AbstractOptParser {
opt[File]('r', "refFlat") required () valueName "<file>" action { (x, c) =>
c.copy(refFlat = x)
- }
+ } text "refFlat file. Mandatory"
opt[File]('o', "outputDir") required () valueName "<directory>" action { (x, c) =>
c.copy(outputDir = x)
- }
+ } text "Output directory. Mandatory"
opt[File]('b', "bam") required () valueName "<file>" action { (x, c) =>
c.copy(bamFile = x)
- }
+ } text "Bam file. Mandatory"
opt[String]('p', "prefix") valueName "<prefix>" action { (x, c) =>
c.copy(prefix = x)
}
--
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