I don't know what you can get from a .mxf file, but you seem to be saying you know how to get a Pronto Hex string (the only format you can use as input to IrTool).

If you have a Pronto Hex string, then you need the JP1 group's version of the IrTool program and you need DecodeIr.dll

DecodeIr is available on Rob's web site in:
[Link: hifi-remote.com]

The Jp1 version of IrTool is in
[Link: groups.yahoo.com]
(for that one, you need to join the Yahoo JP1 forum).

If you use the right IRTool and it finds DecodeIr.dll it will display the decode in current JP1 terminology (and then redisplay it the old way, which you can ignore).