How do I clone my old mac to a new one? I have a MacBook Pro running Lion 10.7.5.  I just got a new mac running Yosemite. I have everything from the old mac backed-up on Time Machine. How do I transfer all my files, apps, email, photos in iPhoto, music, etc., to the new mac? I want to get everything I have on my old mac, plus anything new on the new mac, such as new apps.

Will the old Lion OS get installed on the new mac when I use the migration tool? I do not want that!
If you haven't set up the new machine yet, you can do this by connecting your Time Machine drive before booting. (If the backup is on a Time Capsule, it will search for backups on it.) During the setup of the new machine, you'll be presented with the option of migrating your setup from the Time Machine backup.

If you've already configured the new Mac, use the Migration Assistant (Applications->Utilities) to do the same; or reboot into Recovery Mode to restore from the Time Machine backup. I'd actually do a full system reinstall and migration from the Time Machine backup in Recovery Mode to prevent any issues.