As an alternative to Ralackk's answer, you could get a port to run it in (e.g. EDuke32). When using EDuke32 you can change the keyboard mappings and mouse control options from the game's menu system.
What is Eduke32 and by port what do you mean? The game was ported to a newer OS?
Google will show you EDuke32 in a snap.
But to put it simply, Duke Nukem 3D was created in the Build engine and is a DOS game. To get it working in Windows, GOG have bundled it with the DOSBox emulator, so that DOS is emulated in order to play the game.
The source code for the game was released some years ago and this allowed people to create new engines to run the game, such as EDuke32.
The advantage of EDuke32 is that it is written for Windows, it does not work in DOS, so runs natively on modern Windows. Also, it allows you to use high resolution packs and 3D models, higher screen resolutions to run the game in, polymer lighting, widescreen, and more.