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You are correct that trying to pass in xacro is not working - the URDF parser will just ignore everything that's in xacro, which is why you are only getting your base link, as that's in urdf. To convert from xacro to urdf run the following command:

rosrun xacro xacro.py my_robot.xacro > my_robot.urdf

Replacing my_robot, of course, and then run the wizard with my_robot.urdf .