This is not possible to specify the image pattern right now, I guess this command works with RGGB by default.
Anyway, it should be possible to tweak the image geometry a little bit before and after to make the input follow the RGGB pattern before the reconstruction. For instance, you can add or remove the first column and/or the first row when necessary:
For GBRG : $ gmic test.raw,uchar,640,480,1 -rows. -1,100%
For GRBG : $ gmic test.raw,uchar,640,480,1 -columns -1,100%
For BGGR : $ gmic test.raw,uchar,640,480,1 -crop -1,-1,100%,100%