Here is how I was able to solve this problem.
In the source transformer I defined "Start of File" and "End of File" variables like this:
channelMap.put('SOF',String.fromCharCode(11)); // Start Of File: returns \v (vertical tab));
channelMap.put('EOF',String.fromCharCode(28,13)); // End Of File: returns <FS><CR>);
In the destination template I then did this:
${SOF}${message.encodedData}${EOF}
I wrote the messages out to temporary file and opened them in a Hex Editor. I was able to confirm that the a 0x0B
(Ascii 11) was written prior to the message and the message closed with 0x1C
0x0D
(Ascii 28, Ascii 13)