Whole Wheat Flower

You will want to use either cake, pastry or all purpose flour for your cookies.
whole wheat has less gluten formation and will leave your cookies to dence.
you can add a portion say 15% whole wheat flour in place of the same portion of the above mentioned flours.

What is your formula?

I don't even quite understand this question. What is it you're trying to do?

If you include the entire formula you are using then we are better able to help. The method in which you mix your cookie dough also has an effect on the final outcome. If you substitute sugar with honey or agave nectar that will have an effect on the texture of the cookie also.

I'm a little at a loss to what you mean by "like a cake," do you mean "chewy?" Or, do you mean "light and airy?"

Chef peon made some excellent points.

As chefpeon wrote: Always a help, especially with baking. Most especially when the description of the problem is ambiguous.

Yes to this as well.

Sugar has the effect of making cookies crisp, compared to either honey or agave. More likely than not, this is at least partly why you get "like a cake" cookies -- if by "like a cake" you mean chewy.

Another possibility is that you're baking at too low a temperature, and yet another is that you're not cooking all the way through. In fact, the first suggestion I'd make (other than changing the ingredients) is to cook a little longer at a slightly higher temperature.

Most bakers expect a substitution of whole wheat for white flour to result in a much heavier cookie (or any other baked good, for that matter); and heavier is not consistent with "like a cake," at least not in the way most of us think of cake. That may account for some of the confusion. On the other hand, if by "like a cake" you mean "light and fluffy," we all want to know your secret.

If you could be more specific about your recipe -- in terms of ingredients, techniques, times and temperatures -- and perhaps try another description of what you're going for and what you're getting which doesn't include a comparison to cake, it could help us help you.

Finally, as a general rule, oatmeal cookies are supposed to be and are generally expected to be chewy and not crisp -- this has everything to do with the nature of oatmeal and the type of sweeteners (molasses, brown sugar) usually employed.

Keep on experimenting and stay in touch,
BDL

Wow... I think I'm the only person here that understand's what you mean by "like a cake"!
I've experimented alot with cakey cookies, they're one of my favourite textures to play with; you need a lighter batter (hence more water) and egg yolks. The more egg yolks the more cake-like the texture.
If you DON'T want that then you need to eliminate egg yolks, use a denser batter (more like a dough) that can be chilled and shaped by hand.
Most drop cookies I've tried come out relatively cakey.

Using whole wheat flour shouldn't make a huge difference; it is denser, therefore less of the proteins work, but that's ok as we're not too bothered about the proteins working in cookies anyway; like a cake- we rely on the starch to gelate for structure (although high protein flours spread less), the less/more starch that gelates, the more/less crumbly the texture (this depends on cooking temps/times and mix ingredients).

The idea of creaming the butter with the sugar btw is to incorporate air into the mix (not something you want to do if you don't want cakey cookies) the sugar grains join to air molecules on the whisk as its moving through the mix- this wouldn't happen with honey or nectar (but maybe thats a good thing for you), but it won't effect the chocolate's ability to set.
Check your chocolate, if you're having problems, maybe you're using a high-fat chocolate (too much cocoa butter) and its spreading into the mix- use a darker baking chocolate and it'll be firmer.

I wouldn't worry about using whole wheat flour, but I would reccommend doing some research on the differences in textures in cookies and how to get them. Knowledge is power! (i've always wanted to say that!)

just be careful with the whole wheat flour as it will not bake "up" like cake flour will and it will take in the moisture making a dense, heavy cookie.