In the bowl of a stand mixer fitted with the dough hook, add water, then sprinkle with the yeast. Allow to sit 5 minutes. The yeast should turn frothy. Add the olive oil, sugar, and salt and mix. Add the whole wheat flour and mix again. With the motor running, add the all-purpose flour a little at a time until the desired consistency is reached. The dough should pull away from the sides and bottom of the bowl. It may still be a little tacky, but should not completely stick to your fingers, nor should it crumble or break into pieces.
Transfer dough to a floured counter or board and knead a few minutes before forming into a tight ball. Place the dough ball in a large greased or oiled bowl and cover with a sheet of plastic wrap that has been sprayed with non-stick spray. Place the bowl in a warm spot until doubled in size, about 1 1/2 hours.
Preheat the oven to 400ºF. Dust a large baking sheet with cornmeal.
Punch the dough down and cut it in half, reserving one half for another use. Using your hands, gently stretch the dough into a square a bit before placing it on the baking sheet and continuing to spread it out.
Spread the pizza with the pizza sauce, then sprinkle on the mozzarella. Evenly distribute the onion and pepper, then sprinkle with the Parmesan cheese. Add crushed red pepper flakes and black pepper to taste.
Bake 10 minutes or until the crust is beginning to brown and the cheese is melted. Slice and serve.