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There are 2 ways to model subsurfaces in E+: simplified and detailed. For the detailed mode you will use the FenestrationSurface:Detailed object (regardless if you are modelling windows, doors or glazed doors). In this case the subsurface is defined geometrically, through the coordinates of each vertex. In the simplified mode you will have a different object, depending on the subsurface type (window, door, glazed door,...). You will input it through few geometrical information and you will be only able to model rectangular subsurfaces. In both cases you will be able to assign constructions, shading, frame, etc to your subsurface.
As default, Euclid will input your subsurface in the detailed mode. If this is the object you are using, then you should check the "Surface type" field and be sure to set it to "GlassDoor". Then it will allow you to use transparent materials. If you use the "Door" type, you can only assign opaque materials to it. However, you will find detailed information about it in the InputOutputReference.
If you are interested in other ways to model windows or glass doors in EnergyPlus, you should have a look at the WINDOW program, that allows you to model your windows and then export them as E+ objects (here).