From 7bd5c5b1e9edac17590a14d65a8ccbba26a64c21 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 15 Apr 2016 16:09:06 +0200
Subject: [PATCH] Adding descriptive help to the commandline help
---
.../biopet/core/report/ReportBuilder.scala | 20 ++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
index 9eea22210..41a974fcc 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
@@ -24,6 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.Input
import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
import scala.collection.mutable
+import scala.language.postfixOps
/**
* This trait is meant to make an extension for a report object
@@ -66,15 +67,28 @@ trait ReportBuilderExtension extends ToolCommandFunction {
trait ReportBuilder extends ToolCommand {
- case class Args(summary: File = null, outputDir: File = null, pageArgs: mutable.Map[String, Any] = mutable.Map()) extends AbstractArgs
+ case class Args(summary: File = null,
+ outputDir: File = null,
+ pageArgs: mutable.Map[String, Any] = mutable.Map()) extends AbstractArgs
class OptParser extends AbstractOptParser {
+
+ head(
+ s"""
+ |$commandName - Generate HTML formatted report from a biopet summary.json
+ """.stripMargin
+ )
+
opt[File]('s', "summary") unbounded () required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(summary = x)
- }
+ } validate {
+ x => if (x.exists) success else failure("Summary JSON file not found!")
+ } text "Biopet summary JSON file"
+
opt[File]('o', "outputDir") unbounded () required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(outputDir = x)
- }
+ } text "Output HTML report files to this directory"
+
opt[Map[String, String]]('a', "args") unbounded () action { (x, c) =>
c.copy(pageArgs = c.pageArgs ++ x)
}
--
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