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You have a few options for mapping geomagic touch to control the arm. You can either try doing joint positions like you mentioned, or you could control the end effector position based on the movement of the geomagic touch. It really depends on how you plan on using it.

In either case, you need to make a joint controller. For the first scenario, this would just be joint positions based on the geomagic touch. In the second case you can create a joint trajectory controller in which you send valid trajectories to the controller. You would have to create these trajectories on your own or use some motion planning interface such as MoveIt!

Before doing this, I would make sure you can send a joint position to each joint controller and successfully move the model in Gazebo.