Using whole wheat flour in place of white flour

Whole wheat flour, which is milled from hard wheat, is significantly higher in protein (gluten) than all-purpose flour: 14% vs 10%. Therefore, you run the risk not only of your cookies being tough, but also excessively dry. A greater rate of hydration is necessary to keep the WW flour from pulling all available moisture from your dough in order to hydrate the higher amount of protein. I would suggest using WW pastry flour, which is milled from soft wheat, and has a protein content of about 10%, equal to that of AP flour. It will give you more fiber, if that is what you are anticipating, while still yielding a typically tender cookie. As others have suggested, start with a 50-50 blend, and see how you like it. Adjust the ratio up or down from there.

Thanks for your help! I went with the http://food52.com/recipes/2301_crispy_oatmeal_cookies_with_pecans_and_chocolate_chips. I used regular whole wheat flour. They are delicious!

Unless using a recipe specifically designed that way, you should never replace more than half the white flour with whole-wheat; there will not be enough gluten to support the structure the recipe was designed for.

If you want to make chocolate chip cookies w/o white flour, I wholeheartedly recommend Kim Boyce's (Good to the Grain, Piglet winner a few years ago) recipe. Her recipe produces delicioius cookies with a great, not at all grainy, texture and a wonderful chocolatey flavor. http://www.culinate.com/books/collections/all_books/good_to_the_grain/chocolate_chip_cookies. This recipe is in the regular rotation in my kitchen.

I agree with trying half white and half whole wheat first. Or you could try this recipe which uses white whole wheat flour. (The cookies will be crispy because that's how we like them.)
http://food52.com/recipes/2301_crispy_oatmeal_cookies_with_pecans_and_chocolate_chips

Replacing white flour with whole wheat will probably make the cookies denser, and you might have to add more liquid to the dough to get it the right consistency. If you're set on using whatever recipe you're starting with, I'd try 1/2 and 1/2 to begin with, and if it works out, maybe next time use more. Otherwise, try googling "whole wheat oatmeal chocolate chip cookies"-I know there are plenty of recipes out there where someone's already figured out good ratios of flours.