The full El Cap install app _normally_ is found in the Applications folder.
Not sure why the full app would stay in the App Store folder, which is, in effect, a temp folder for App Store downloads.
You could open your App Store, then check the Store menu for "Check for Unfinished Downloads". If anything shows up, that may properly complete that download. Then quit the App Store, and reopen it.
That may clear out that item without you manually deleting it.
But, if it stays through a restart, and a relaunch of the App Store, then certainly manually delete it.