What is best and safe way to optimize all databases on server?

I don't know the best way to do it, but I do it like this:
Code:
mysqlcheck --defaults-extra-file=/usr/local/directadmin/conf/my.cnf --auto-repair --optimize --all-databases

What I would like, is to automatically exclude all innodb-tables from the command, because it is not possible to optimize those, and they are then being recreated instead, and that takes up a lot of time and cpu. It might not be possible exclude innodb in the command, but if somone know how to, please share it here. :)
 
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