Pre-heat oven to 350 degrees and line baking sheet with parchment paper.
Add rolled oats to a food processor and grind until they're a fine powder.
In a stand mixer cream together butter, sugar, and brown sugar on medium speed until light and fluffy.
Add in egg and vanilla until well combined.
Add in applesauce until smooth.
Sift together oat flour (your ground oats), whole-wheat flour, baking soda, and salt.
Add to the stand mixer on the lowest setting until just combined.
Fold in the pretzels.
Place the chocolate chips in a small bowl and scoop 18 balls of dough (just shy of 2 tablespoons) onto a large plate.
Roll each ball of cookie dough in a small amount of chocolate chips until they're all rolled and you run out of the remaining chips.
Refrigerate the dough for 20 minutes.
Bake for 12-14 minutes, 6 to a regular-sized cookie sheet (bake in batches, keep cookie dough in the refrigerator while other cookies are baking).