You can run topas from the command line with:

c:>tc file.inp [>file.out]

This always works if you run from the main topas directory, it might work from other directories!

A useful tip to add information to the inp file at run time is:

tc test_examples\y2o3a.inp "macro aac$ { iters 3000 }"

The macro called “aac$” is a special macro that instructs the program to place what's in aac$ at the bottom of the INP file. Other macros are on the page on automating_multiple_refinements.