Preheat oven to 375. Prepare a 13 x 9" pan with cooking spray; set aside. Cook rigatoni pasta according to package directions. Drain and return to pot. In a skillet, heat oil over medium heat. Add onions, bell peppers, garlic and mushrooms. Cook until tender. Add crushed tomatoes, tomatoes and green chilies, and black pepper. Heat to a boil and then reduce heat. Stir occasionally and simmer 15 minutes. Add sauce, cottage cheese, and half mozzarella cheese into pasta. Pour into prepared pan. Sprinkle with remaining cheese. Cover and bake for 20 minutes, or until heated through.