Preheat oven to 350F and line a baking sheet with parchment paper.
In a medium bowl, stir together oats, flours, baking powder, baking soda, and salt.
In a large bowl, cream together the butter and the sugars until fluffy. Beat in the eggs, then the applesauce and the vanilla extract. Stir in the oat/flour mixture until just combined. Stir in the chocolate chips.
Drop 1/4-cupfuls of the dough onto the prepared baking sheet, flattening each cookie slightly. Bake for about 12-15 min. Cookies will be light brown at the edges when done.
Let cool on sheet for 3 or 4 minutes, then transfer to a wire rack to cool completely.