diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
index efacde231..12bf548d5 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
@@ -159,6 +159,22 @@ public class ArgumentSource {
         return field.isAnnotationPresent(Advanced.class);
     }
 
+    /**
+     * Is the given argument an output.
+     * @return True if so. False otherwise.
+     */
+    public boolean isOutput() {
+        return field.isAnnotationPresent(Output.class);
+    }
+
+    /**
+     * Is the given argument an input.
+     * @return True if so. False otherwise.
+     */
+    public boolean isInput() {
+        return field.isAnnotationPresent(Input.class);
+    }
+
     /**
      * Is this command-line argument dependent on some primitive argument types?
      * @return True if this command-line argument depends on other arguments; false otherwise.
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index 01221cf27..893a8349b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -194,11 +194,26 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     @Requires("argumentSource != null")
     @Ensures("result != null")
     private String docKindOfArg(ArgumentSource argumentSource) {
-        if (argumentSource.isRequired()) return "required";
-        else if (argumentSource.isAdvanced()) return "advanced";
+        if (argumentSource.isRequired()) {
+            if (argumentSource.isInput()) return "required_in";
+            else if (argumentSource.isOutput()) return "required_out";
+            else if (argumentSource.isFlag()) return "required_flag";
+            else return "required_param";
+            }
+        else if (argumentSource.isAdvanced()) {
+            if (argumentSource.isInput()) return "advanced_in";
+            else if (argumentSource.isOutput()) return "advanced_out";
+            else if (argumentSource.isFlag()) return "advanced_flag";
+            else return "advanced_param";
+        }
         else if (argumentSource.isHidden()) return "hidden";
-        else if (argumentSource.isDeprecated()) return "depreciated";
-        else return "optional";
+        else if (argumentSource.isDeprecated()) return "deprecated";
+        else {
+            if (argumentSource.isInput()) return "optional_in";
+            else if (argumentSource.isOutput()) return "optional_out";
+            else if (argumentSource.isFlag()) return "optional_flag";
+            else return "optional_param";
+        }
     }
 
     /**
@@ -238,11 +253,20 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     private Map<String, List<Map<String, Object>>> createArgumentMap() {
         Map<String, List<Map<String, Object>>> args = new HashMap<String, List<Map<String, Object>>>();
         args.put("all", new ArrayList<Map<String, Object>>());
-        args.put("required", new ArrayList<Map<String, Object>>());
-        args.put("optional", new ArrayList<Map<String, Object>>());
-        args.put("advanced", new ArrayList<Map<String, Object>>());
+        args.put("required_in", new ArrayList<Map<String, Object>>());
+        args.put("required_out", new ArrayList<Map<String, Object>>());
+        args.put("required_param", new ArrayList<Map<String, Object>>());
+        args.put("required_flag", new ArrayList<Map<String, Object>>());
+        args.put("optional_in", new ArrayList<Map<String, Object>>());
+        args.put("optional_out", new ArrayList<Map<String, Object>>());
+        args.put("optional_param", new ArrayList<Map<String, Object>>());
+        args.put("optional_flag", new ArrayList<Map<String, Object>>());
+        args.put("advanced_in", new ArrayList<Map<String, Object>>());
+        args.put("advanced_out", new ArrayList<Map<String, Object>>());
+        args.put("advanced_param", new ArrayList<Map<String, Object>>());
+        args.put("advanced_flag", new ArrayList<Map<String, Object>>());
         args.put("hidden", new ArrayList<Map<String, Object>>());
-        args.put("depreciated", new ArrayList<Map<String, Object>>());
+        args.put("deprecated", new ArrayList<Map<String, Object>>());
         return args;
     }
 
@@ -843,7 +867,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         // general attributes
         List<String> attributes = new ArrayList<String>();
         if (def.required) attributes.add("required");
-        if (source.isDeprecated()) attributes.add("depreciated");
+        if (source.isDeprecated()) attributes.add("deprecated");
         if (attributes.size() > 0)
             root.put("attributes", Utils.join(", ", attributes));
 
diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html
index ea9fa2d72..098d294cb 100644
--- a/settings/helpTemplates/generic.template.html
+++ b/settings/helpTemplates/generic.template.html
@@ -235,11 +235,20 @@
 					</tr>
 					</thead>
 					<tbody>
-					<@argumentlist name="Required" myargs=arguments.required/>
-					<@argumentlist name="Optional" myargs=arguments.optional/>
-					<@argumentlist name="Advanced" myargs=arguments.advanced/>
+					<@argumentlist name="Required Inputs" myargs=arguments.required_in/>
+					<@argumentlist name="Required Outputs" myargs=arguments.required_out/>
+					<@argumentlist name="Required Parameters" myargs=arguments.required_param/>
+					<@argumentlist name="Required Flags" myargs=arguments.required_flag/>
+					<@argumentlist name="Optional Inputs" myargs=arguments.optional_in/>
+					<@argumentlist name="Optional Outputs" myargs=arguments.optional_out/>
+					<@argumentlist name="Optional Parameters" myargs=arguments.optional_param/>
+					<@argumentlist name="Optional Flags" myargs=arguments.optional_flag/>
+					<@argumentlist name="Advanced Inputs" myargs=arguments.advanced_in/>
+					<@argumentlist name="Advanced Outputs" myargs=arguments.advanced_out/>
+					<@argumentlist name="Advanced Parameters" myargs=arguments.advanced_param/>
+					<@argumentlist name="Advanced Flags" myargs=arguments.advanced_flag/>
 					<@argumentlist name="Hidden" myargs=arguments.hidden/>
-					<@argumentlist name="Depreciated" myargs=arguments.depreciated/>
+					<@argumentlist name="Deprecated" myargs=arguments.deprecated/>
 					</tbody>
 				</table>
 			</#if>