You could try to write this line (not tested):
sh "/path/to/myScript.sh" {wav}
You need to make sure that the script has execution rights and that it can take the argument into account
But you will have a problem if you separate the original mono sample into a stereo sample in your script. Polyphone will reload the exported mono sample itself after the script has been run: all extra files that would have been created will be ignored.