How can I use the Simulink coder to create standalone applicatnoi of model that gets variable values from a matlab function .m file?

I have a matlab .m file that takes user input from an excel sheet, does calculations, and then sets the values of variables in a simulink model. The simulink model then returns values to the .m function that then saves data back in excel. I want to make this into a stand alone application using the compiler, Simulink coder toolboxes. However I get an error when I try to use the simulink coder because the simulink model has variables that are not defined until the .m file is ran. Can I compile the simulink model with variables not defined in the model?