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If your GIS application is asking for a serial port, I'm assuming that it expects live GPS data in whatever raw format coming from the antenna. However, your bagfile contains data in the format that ROS uses to pass messages around, and those aren't going to be trivially compatible.
Does your GIS application have an option to load in pre-recorded data? If so, you might be able to write a simple node that subscribes to the /GPSFix messages and outputs a properly formatted file.
Alternatively, you're probably going to be stuck writing a node that pretends to be a GPS receiver, listening to the /GPSFix messages and emitting that data as properly-formatted serial packets. I haven't done it, but SO suggests that you can fake a serial connection.
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