This is a test that covers the ViPR use case for protein with a defaultprotein matrix settingsetting:

tool=RAXMLHPC2_TGB
vparam.runtime_=168 (we use cipres run wall time as suggested by you)
vparam.bootstrap_seed_=0 
vparam.bootstop_=<boot strap number that user specified from web interface if it's not 100>
vparam.dna_gtrcat_=GTRGAMMA for dna sequences; for protein sequences, we use the following two:
vparam.prot_sub_model_=PROTGAMMA
vparam.prot_matrix_spec_=<protein matrix that user specified from web interface>

At present we must set vparam.bootstrap_seed_=0

Generates this command line:
raxmlHPC-PTHREADS      -n result -s infile.txt  -m PROTGAMMADAYHOFF   -p 12345      '