Yes, you can do this, however you need to run the GUI MegaWizard once to create the retrieval information (at the bottom of the generated .v or .vhd instance file). Once you have this, you can copy just the retrieval info from the file and save it to a file <filename>. Then from the command line, you can type "qmegawiz -silent <filename>", and it should run the MegaWizard from the command line without any output to the console and without opening the GUI. You can now modify the parameters in the retrieval info in <filename> and re-run qmegawiz and it will recreate the files with your changes.