If you want to execute perl script.pl (with some additional parameters) on the remove server, you have to get script.pl there (just as you have to get perl there, if it isn't there already). When it's there, you can do:

    $ ssh user@server "perl /path/to/script.pl $cmdlinArgtoscrpt"
[download]

Where I assume that $cmdlinArgtoscrpt contains the arguments to the script.