Q: I have the Mac Pro Quad-Core 2.93 GHz Nehalem. I could not get the latest OS X El Capitan to be available in my App Store.

According to the specs for El Capitan you should be able to upgrade. What happens when you type El Capitan into the search bar on AppStore?

EDIT: Or are you running 10.11.x and looking for an update? Try here Apple - Support - Downloads

At this writing, 10.11.2 IS the latest version available to the general public.

There may be some later-numbered versions being tested, but you must be a member of the Beta Test team and you must sign a non-disclosure agreement (among other terms and conditions) to be given access to that software.