Batch processing with command window inputs

I have a P-file that, when run, prompts the user to enter the name of a .m file that contains a number of parameters the program requires to operate. In normal use, the user enters the filename in the command window and hits enter. I would like to make a script that runs this program with several different inputs, as the number of iterations required makes manual data entry impractical.

So far, I have not found any way to make a script that can give the program the input that it needs to continue. Loading the required variables to the workspace is probably adequate, but the program still prompts the user for input and will not perform the calculations until it has received input.

Is there any way I can automate this data entry process?