You'd set up a cron job to run the CLI-command to call your script. You could either do something like:
wget http://localhost/file.php
which would probably work best, since you have it set up for the web. Otherwise, you could rewrite it as a php shell script and call it as
/path/to/file/file.php
which would cause your shell (bash, most likely) to interpret it as a php shell script. Or, you could call it with command-line php mode:
php /path/to/file/file.php
or something along those lines. It's just like setting up a regular cronjob though - just pick which way you want to execute it.