From fce5cb9f351f2c232580bafd8be560e2adcb8014 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 25 Jul 2012 17:23:02 -0400
Subject: [PATCH] Few category changes

---
 .../src/org/broadinstitute/sting/gatk/CommandLineGATK.java | 7 +++----
 .../src/org/broadinstitute/sting/gatk/walkers/Walker.java  | 5 +----
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index d8674c606..b1ad19e69 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -44,16 +44,15 @@ import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import java.util.*;
 
 /**
+ * All command line parameters accepted by all tools in the GATK.
+ *
  * The GATK engine itself.  Manages map/reduce data access and runs walkers.
  *
  * We run command line GATK programs using this class.  It gets the command line args, parses them, and hands the
  * gatk all the parsed out information.  Pretty much anything dealing with the underlying system should go here,
  * the gatk engine should  deal with any data related information.
  */
-@DocumentedGATKFeature(
-        groupName = "GATK Engine",
-        summary = "Features and arguments for the GATK engine itself, available to all walkers.",
-        extraDocs = { UserException.class })
+@DocumentedGATKFeature(groupName = "GATK Engine")
 public class CommandLineGATK extends CommandLineExecutable {
     @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
     private String analysisName = null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
index 18c383ed9..6cd2e8aea 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
@@ -49,10 +49,7 @@ import java.util.List;
 @ReadFilters(MalformedReadFilter.class)
 @PartitionBy(PartitionType.NONE)
 @BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
-@DocumentedGATKFeature(
-        groupName = "GATK walkers",
-        summary = "General tools available for running on the command line as part of the GATK package",
-        extraDocs = {CommandLineGATK.class})
+@DocumentedGATKFeature(groupName = "Uncategorized", extraDocs = {CommandLineGATK.class})
 public abstract class Walker<MapType, ReduceType> {
     final protected static Logger logger = Logger.getLogger(Walker.class);
     private GenomeAnalysisEngine toolkit;