Apple prefers you to upgrade to the latest macOS which would be High Sierra now on version 10.13.2. Thus the refusal to install El Capitan. If you have or know of another mac that has downloaded El Capitan previously you may be able to download it via the Purchases page of the App Store and transfer Install Mac OS X El Capitan.app from Applications folder of the donor mac to your Mac Pro. This is also true of a mac that has not upgraded to El Capitan, but cannot upgrade to Sierra or High Sierra.
When Apple releases the latest macOS the previous versions are removed from the App Store, however because of some app compatibility issues Apple have continued to offer Sierra, How to download macOS Sierra - Apple Support
if you choose to download this it will install version 10.12.6, you would then check the App Store for any subsequent security updates etc.
Updates you see on the Apple Support Downloads site need an existing version of the OS you are updating to.
Combo updates will update any previous version of the titled OS. Incremental (Delta) updates will update from a previous version of an OS to the next numbered version.
Whatever version of OS upgrade you download make a copy of the installer app. Once the download has completed and before going ahead with the installation look inside your Applications folder for Install macOS Sierra.app (or other similarly named .app depending on what OS you downloaded) make a copy of this somewhere else on your mac or external drive or USB stick. Having this is handy if you want to install on other macs or if you need to reinstall the OS due to a problem, saves having to download it again. You can also use it to create a bootable USB, How to create a bootable installer for macOS - Apple Support
