Merge branch 'vep_docfix' into 'develop'

add more info to VepNormalizer tool help

self-explanatory.

See merge request !157

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala

@@ -239,25 +239,24 @@ object VepNormalizer extends ToolCommand {
       c.copy(inputVCF = x)
     } validate {
       x => if (x.exists) success else failure("Input VCF not found")
-    } text "Input VCF file"
-
+    } text "Input VCF file. Required."
     opt[File]('O', "OutputFile") required () valueName "<vcf>" action { (x, c) =>
       c.copy(outputVCF = x)
     } validate {
       x =>
         if (!x.getName.endsWith(".vcf") && (!x.getName.endsWith(".vcf.gz")) && (!x.getName.endsWith(".bcf")))
           failure("Unsupported output file type") else success
-    } text "Output VCF file"
+    } text "Output VCF file. Required."
 
     opt[String]('m', "mode") required () valueName "<mode>" action { (x, c) =>
       c.copy(mode = x)
     } validate {
       x => if (x == "explode") success else if (x == "standard") success else failure("Unsupported mode")
-    } text "Mode"
+    } text "Mode. Can choose between <standard> (generates standard vcf) and <explode> (generates new record for each transcript). Required."
 
     opt[Unit]("do-not-remove") action { (x, c) =>
       c.copy(removeCSQ = false)
-    } text "Do not remove CSQ tag"
+    } text "Do not remove CSQ tag. Optional"
   }
 }