Added examples that can be cut and pasted.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@227 348d0f76-0448-11de-a6fe-93d51630548a

doc/GATK_User_Manual.tex

@@ -32,8 +32,28 @@ member variables annotated with @Argument in the walker.  The
   \item [exclusive] Specifies that this argument is mutually
     exclusive of another argument in the same walker.  Defaults to not
     mutually exclusive of any other arguments.
+  \item [defaultValue] Specifies the default value for this parameter,
+    in string form.  
 \end{enumerate}
 
+Examples:
+
+Create an required int parameter with full name --myint, short name
+-m.
+Pass this argument by adding ``--myint 6'' or -m6 to the command line.
+\begin{verbatim}
+@Argument
+public int myInt;
+\end{verbatim}
+
+Create an optional float parameter with full name
+--myFloatingPointArgument, short name -m.  Pass this argument by
+adding --myFloatingPointArgument 2.71 or -m2.71.
+\begin{verbatim}
+@Argument(fullName="myFloatingPointArgument",required=false,defaultValue="3.14159")
+public float myFloat;
+\end{verbatim}
+
 The GATK will parse the argument differently depending on the type of
 the public member variable's type.  Many different argument types are 
 supported, including primitives and their wrappers, arrays, typed and