(Note: I'm not a lawyer.)
From the Free Software Foundation's GPL FAQ:
If a programming language interpreter has a license that is incompatible with the GPL, can I run GPL-covered programs on it?
When the interpreter just interprets a language, the answer is yes. The interpreted program, to the interpreter, is just data; the GPL doesn't restrict what tools you process the program with.
It would seem that the "it's just data" argument applies in your case as well. The GPL's copyleft provisions only apply when the GPL'd work and some other work form a derivative work, which doesn't appear to happen in your case.
Of course, any GPL work you distribute must stay under the GPL, but the GPL provisions will not apply to your project as a whole, because it doesn't combine with your existing work into a new derived work.
