There are a number of ways to do this. If you want to change all desert categories to agriculture land, simply modify the LANDUSE.TBL and/or VEGPARM.TBL to change the physics properties from desert to the land category you would like to use. If you would like to only change the desert area in part of your domain, you may have to use read_wrf_nc.f and an NCL script that reads and writes data out after modification. To use read_wrf_nc.f, see information in the User's Guide (Chapter 10). For NCL, see this tutorial talk on NCL:
http://www2.mmm.ucar.edu/wrf/users/tutorial/201807/jaye_ncl.pdf
If you modify input data to program REAL, use the namelist option surface_input_source=3 to avoid recalculation of dominant land categories (LU_INDEX).
http://www2.mmm.ucar.edu/wrf/users/tutorial/201807/jaye_ncl.pdf
If you modify input data to program REAL, use the namelist option surface_input_source=3 to avoid recalculation of dominant land categories (LU_INDEX).