To make the dough, mix the flours with a pinch of salt. Dissolve the yeast in a half-cup of the tepid water. Add the mixture to the flour little by little, kneading until the mixture is uniform and doesn’t stick to your hands. Add more water if necessary. Cover with a cloth and let stand for one hour.
Meanwhile, steam the cockles until they open. Remove from heat and let cool. Remove the meat from the shells and reserve.
In a frying pan over medium-high heat, heat 4 tablespoons of oil. Add the onion and sauté until soft but not browned. Add the paprika and a pinch of salt and stir well. Then add the grated tomato and cook, stirring, until the liquid has evaporated. Remove from heat and reserve.
To assemble the pie, grease a large baking pan. Slick your hands in a light coating of oil and take out a small portion of the dough. Flatten it between your hands as thin as possible and put it in the pan. Take out another portion of the dough, and continue in the same way. (It will be a little crumbly.) Put it next to the previous piece of dough, using your finger or a fork to bind them together. Repeat until the dough covers the bottom of the baking pan. Cover with half of the onion mixture and top with the cockles. Put the rest of the onion on top of the cockles.
To cover the empanada, create a crust in the same way that you made the base, and cover the filling. Drizzle a healthy amount of olive oil on top, and cut the pie into serving pieces. Bake the empanada at 375° for 40 minutes, or until golden brown. Serve warm or room temperature.