Enumerated types are working.

public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java

@@ -154,9 +154,13 @@ public class GATKRunReport {
     private long nReads;
 
     public enum PhoneHomeOption {
+        /** Disable phone home */
         NO_ET,
+        /** Standard option.  Writes to local repository if it can be found, or S3 otherwise */
         STANDARD,
+        /** Force output to STDOUT.  For debugging only */
         STDOUT,
+        /** Force output to S3.  For debugging only */
         AWS_S3   // todo -- remove me -- really just for testing purposes
     }
 

public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java

@@ -221,10 +221,10 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
     protected Map<String, Object> docForArgument(FieldDoc fieldDoc, ArgumentSource source, ArgumentDefinition def) {
         Map<String, Object> root = new HashMap<String, Object>();
-        root.put("name", def.fullName != null ? "--" + def.fullName : "-" + def.shortName);
+        root.put("name", def.shortName != null ? "-" + def.shortName : "--" + def.fullName );
 
-        if ( def.fullName != null && def.shortName != null)
-            root.put("synonyms", def.fullName != null ? "--" + def.fullName : "-" + def.shortName);
+        if ( def.shortName != null && def.fullName != null )
+            root.put("synonyms", "--" + def.fullName);
 
         root.put("required", def.required ? "yes" : "no");
         root.put("type", def.argumentType.getSimpleName());

settings/helpTemplates/generic.template.html

@@ -2,11 +2,10 @@
 
 <#macro argumentlist name myargs>
     <#if myargs?size != 0> 
-        <tr><th colspan="4"><b>${name}</b></th></tr>
+        <tr><th colspan="3" id="row-divider">${name}</th></tr>
         <#list myargs as arg>
             <tr>
                 <td><a href="#${arg.name}">${arg.name}</a></td>
-                <td><a href="#${arg.name}">${arg.synonyms!""}</a></td>
                 <td>${arg.type}</td>
                 <td>${arg.summary}</td>
             </tr>
@@ -22,7 +21,7 @@
     (<#if arg.attributes??>${arg.attributes} </#if>${arg.type})</h3>
     ${arg.summary}. ${arg.fulltext}<br>
     <#if arg.options??>
-        <p>The ${arg.name} argument can have one of the following values:</p>
+        <p>The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:</p>
         <dl class="enum">
         <#list arg.options as option>
             <dt>${option.name}
@@ -70,7 +69,6 @@
       <thead>
       <tr>
          <th>Name</th>
-         <th>Synonyms</th>
          <th>Type</th>
          <th>Summary</th>
       </tr>

settings/helpTemplates/style.css

@@ -19,47 +19,12 @@ p.version, p.see-also
 	font-size: 8pt;
 }
 
-dl.enum
-{
-	margin: 0em 0;
-	padding: 0;
-}
-
-.enum dt
-{
-	position: relative;
-	left: 0;
-	top: 1.1em;
-	width: 5em;
-	font-weight: bold;
-}
-
-.enum dd
-{
-	border-left: 1px solid #000;
-	margin: 0 0 0 6em;
-	padding: 0 0 .5em .5em;
-}
-
-/*
-a
-{
-	color: #546188;
-	text-decoration: none;
-}
-
-a:visited 
-{
-	color: #546188;
-}
-*/
-
 h1, h2, h3
 {
 	font-family: Corbel, Arial, Helvetica, Sans-Serif;
 	font-weight: bold;
 	text-align: left;
-	color: #bac8da;
+	color: #669;
 }
 
 h1
@@ -74,16 +39,27 @@ h3
 	font-weight: normal;
 }
 
-table.indextable tr td
-{
-	margin-right: 1em;
-}
-
-/* 
-	Blue Dream
-	Written by Teylor Feliz  http://www.admixweb.com
+/*
+ * enum DT layout
 */
 
+dl {
+   border: 1px solid #ccc;
+}
+
+dt {
+    font-weight: bold;
+    text-decoration: underline;
+}
+
+dd {
+    margin: 0;
+    padding: 0 0 0.5em 0;
+}
+
+/*
+ * clean table layouts
+*/
 #hor-minimalist-b
 {
 	font-family: "Lucida Sans Unicode", "Lucida Grande", Sans-Serif;
@@ -111,4 +87,10 @@ table.indextable tr td
 #hor-minimalist-b tbody tr:hover td
 {
 	color: #009;
+}
+
+th#row-divider 
+{
+    font-weight: bolder;
+	font-size: larger;
 }