This test covers the ViPR use case where a non-default protein matrix is used with bootstrapping:

tool=RAXMLHPC2_TGB
vparam.runtime_=168 (we use cipres run wall time as suggested by you)
vparam.bootstrap_seed_=1 (we use bootstrap_seed to indicates bootstrapping, this will be 0 for non-bootstrapping)
vparam.bootstop_=<boot strap number that user specified from web interface if it's not 100>
vparam.prot_sub_model_=PROTGAMMA
vparam.prot_matrix_spec_=<protein matrix that user specified from web interface>

Generates this command line:
raxmlHPC-HYBRID  -n result -s infile.txt -x 12345  -m PROTGAMMALG4M -N 50   -p 12345 -f a