Heat olive oil in a medium nonstick skillet over medium-high heat. Add onion and garlic, and sauté 2 minutes. Add tomato, parsley, and crushed red pepper; cook 3 minutes, and set aside.
Add water and clams to a large Dutch oven over medium-high heat; cover and cook 4 minutes or until shells open. Remove clams from pan, and reserve 3/4 cup cooking liquid. Discard any unopened shells. Cool clams. Remove the meat from shells. Place cooking liquid in pan over medium-high heat until reduced to 1/2 cup (about 5 minutes). Add clams, cooking liquid, and salt to tomato mixture. Serve clam sauce over pasta.