Diffrent shipping conformation mails for different shipping options

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I have following problem, some of my products can not be shipped, the customers have to use "Pick up" as a shipping option and they can pick up their order from our store. Now I would like to have a sepperate Mail for that option, in order to inform the customer that their order is ready for pickup. There is a Mail Template to inform the Customer that their order was shipped. I need a Mail that the order is ready for pick up. My current solution is saying that: "Your order got shipped or is ready for pick up" in one and the same Mail but that is not the solution. It would be great if I had two different Mail Templates for each Shipping option (Shipping, Pick up).
I hope you understood my issue, it would be very nice if you had any solutions. :)