This is a raxml gui command line.
The test provides the command line at the bottom of the page.

raxmlHPC-PTHREADS.exe -T 2 -f A -t "0" -s infile.txt  -m GTRGAMMA -n infile -O -w  "C:/Users/mmiller/Desktop/cipres/raxmlgui/DNA_2/"   
 
RAXMLHPC_TGB_REST
infile_ - Primary Input File
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
datatype_ - Excl - Sequence Type
outgroup_ - String - Outgroup (one or more comma-separated outgroups, see comment for syntax)
constraint_ - InFile - Constraint (-g)
binary_backbone_ - InFile - Binary Backbone (-r)
partition_ - InFile - Use a mixed/partitioned model? (-q)
exclude_file_ - InFile - Create an input file that excludes the range of positions specifed in this file (-E)
invariable_ - Excl - Estimate proportion of invariable sites (GTRGAMMA + I)
prot_matrix_spec_ - Excl - Protein Substitution Matrix
empirical_ - Excl - Use empirical base frequencies?
mlsearch_ - Switch - Find best tree using maximum likelihood search
use_bootstopping_ - Switch - Let RAxML halt bootstrapping automatically (HIGHLY recommended)
printbrlength_ - Switch - Print branch lengths (-k)
all_outputfiles_ - Results -

Job is OK, command line is '
raxmlHPC-PTHREADS (-T 8 will be added by the wrapper)  -f A -n result  -s infile.txt -t tree.tre  -p 12345 -m GTRGAMMA -O 
                                                       -f A -n infile  -s infile.txt -t "0"                -m GTRGAMMA  -O 
                                                       
 -w  "C:/Users/mmiller/Desktop/cipres/raxmlgui/DNA_2/"  is not allowed in cipres

 Test passed.