Cleanup emuns and tables

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

@@ -43,7 +43,7 @@ import java.util.*;
  */
 public class GATKDoclet extends ResourceBundleExtractorDoclet {
     final protected static File SETTINGS_DIR = new File("settings/helpTemplates");
-    final protected static File DESTINATION_DIR = new File("testdoc");
+    final protected static File DESTINATION_DIR = new File("gatkdocs");
     final protected static Logger logger = Logger.getLogger(GATKDoclet.class);
 
     public static class DocWorkUnit implements Comparable<DocWorkUnit> {

settings/helpTemplates/generic.index.template.html

@@ -1,7 +1,7 @@
 <#include "common.html"/>
 
 <#macro emitGroup group>
-  <table border="1" cellpadding="2" width="100%">
+  <table id="hor-minimalist-b">
   <h2>${group.name}</h2>
   <p>
   ${group.summary}  

settings/helpTemplates/generic.template.html

@@ -2,7 +2,7 @@
 
 <#macro argumentlist name myargs>
     <#if myargs?size != 0> 
-        <tr><th colspan="4" align="left">${name}</th></tr>
+        <tr><th colspan="4"><b>${name}</b></th></tr>
         <#list myargs as arg>
             <tr>
                 <td><a href="#${arg.name}">${arg.name}</a></td>
@@ -22,7 +22,7 @@
     (<#if arg.attributes??>${arg.attributes} </#if>${arg.type})</h3>
     ${arg.summary}. ${arg.fulltext}<br>
     <#if arg.options??>
-        <p>Argument is an enumerated type with the following possible values:</p>
+        <p>The ${arg.name} argument can have one of the following values:</p>
         <dl class="enum">
         <#list arg.options as option>
             <dt>${option.name}
@@ -66,17 +66,21 @@
   <#if arguments.all?size != 0> 
       <hr>
       <h2>Feature specific arguments</h2>
-      <table border="1" cellpadding="2" width="100%">
+      <table id="hor-minimalist-b">
+      <thead>
       <tr>
          <th>Name</th>
          <th>Synonyms</th>
          <th>Type</th>
          <th>Summary</th>
       </tr>
+      </thead>
+      <tbody>
          <@argumentlist name="Required" myargs=arguments.required/>
          <@argumentlist name="Optional" myargs=arguments.optional/>
          <@argumentlist name="Hidden" myargs=arguments.hidden/>
          <@argumentlist name="Depreciated" myargs=arguments.depreciated/>
+      </tbody>
       </table>
   </#if>
 

settings/helpTemplates/style.css

@@ -74,29 +74,41 @@ h3
 	font-weight: normal;
 }
 
-#indexheader 
-{
-	position: absolute;
-	left: 50pt;
-	top: 100pt;
-	font-size: 38pt;
-}
-
-#indexbody
-{
-	position: absolute;
-	left: 50pt;
-	top: 180pt;
-}
-
-table#indextable tr td
+table.indextable tr td
 {
 	margin-right: 1em;
 }
 
-tr#indextableheader td
+/* 
+	Blue Dream
+	Written by Teylor Feliz  http://www.admixweb.com
+*/
+
+#hor-minimalist-b
 {
-	font-family: Corbel, Arial, Helvetica, Sans-Serif;
-	font-size: 14pt;
-	font-weight: lighter;
+	font-family: "Lucida Sans Unicode", "Lucida Grande", Sans-Serif;
+	font-size: 12px;
+	background: #fff;
+	margin: 5px;
+	width: 100%;
+	border-collapse: collapse;
+	text-align: left;
 }
+#hor-minimalist-b th
+{
+	font-size: 14px;
+	font-weight: normal;
+	color: #039;
+	padding: 10px 8px;
+	border-bottom: 2px solid #6678b1;
+}
+#hor-minimalist-b td
+{
+	border-bottom: 1px solid #ccc;
+	color: #669;
+	padding: 6px 8px;
+}
+#hor-minimalist-b tbody tr:hover td
+{
+	color: #009;
+}