Preheat the oven to 320˚F. Line cookie sheets with parchment paper and set aside.
In a medium bowl, sift together the flours, baking soda and baking powder.
In a separate bowl, cream together the butter and the sugars until light and fluffy. Beat in the eggs and vanilla. Slowly mix in the flour mixture until fully incorporated. Fold in the chocolate chips and pretzels.
Using a medium cookie scoop, scoop the batter onto a prepared baking sheet. Place 1 whole pretzel on top of each cookie and bake for around 15-17 minutes, or until the edges are browned.