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To prepare cupcakes: Preheat oven to 350°F. Line 12 (1/2-cup) muffin cups with paper liners.
Whisk whole-wheat flour, cake flour, cocoa, baking powder, baking soda and salt in a medium bowl.
Beat granulated sugar and oil in a large mixing bowl with an electric mixer on medium speed until combined. Beat in egg and vanilla until well combined. With the mixer on low, alternately mix in the dry ingredients and buttermilk, starting and ending with dry ingredients and scraping the sides of the bowl as needed, until just combined. Fold in chopped cherries until just combined. Divide the batter among the prepared cups (they will be full).
Bake the cupcakes until a toothpick inserted into the center comes out clean, 22 to 26 minutes. Transfer to a wire rack and let cool completely.
To prepare frosting: Meanwhile, beat cream cheese, sour cream and confectioners’ sugar with an electric mixer until smooth. Refrigerate the frosting until very cold, about 2 hours. Spread the frosting on the cooled cupcakes and decorate with a cherry on top, if desired.