Assimilation of MADIS data is not directly available through WRFDA. However, the WRFDA group 
maintains a conversion utility "MADIS2LITTLER", which converts netCDF MADIS data into LITTLE_R 
format for assimilation in WRFDA (or obs-nudging in WRF). You can find this utility on the web at 
the WRFDA website:

http://www2.mmm.ucar.edu/wrf/users/wrfda/download/madis.html

Compilation and use instructions can be found in the README file provided in that package.