When you use "Run file", the application will be launch the same way as if you doubled click on it.
Run the file at an existing file path. This is analogous to double-clicking the file in the OS file explorer. For executable programs, it will attempt to run the program; for other file types, it will open the default associated program, such as the system default image editor if an image file is given"
I can misunderstood though, does your file do anything while being double-clicked in the explorer? (Maybe it is possible to add command lines in the path)