Few category changes

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;

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;