Menu: Run -> Edit configurations -> "+" (add new config) -> Python.
Script name: program.py
If you need to debug a script from installed packages, such as tox, you can specify the full path too. For example:
Script name: /home/your_user/.envs/env_name/bin/tox
Above /home/your_user/.envs/env_name is a path to virtual environment containing tox package.
Script params: -t input1 -t1 input2