<!-- Bootstrap + Consensus: Two Steps
raxmlHPC-PTHREADS.exe -T 2 -m GTRGAMMA   -n infile.tre -s  infile.txt -O   -x 4 -N 100  -p 368 
&& raxmlHPC-PTHREADS.exe -T 2 -m GTRGAMMA -n con.infile.tre -J MR -z infile.tre  -->

raxmlHPC-HYBRID  -m GTRGAMMA -n boot.tre  -s infile.txt  -O  -x 12345 -N 100  -p 12345    
&& raxmlHPC-PTHREADS -m GTRGAMMA   -n con.tre.tre -J MR -z RAxML_bootstrap.boot.tre '

this workflow succeeds.
NGBW-JOB-RAXMLHPC2_WORKFLOW-A7B707F88071411B809DB951E76236FC (saved)

raxmlHPC-HYBRID -s infile.txt -N 100 -m GTRGAMMA -p 12345  -O -n boot.tre -x 12345   
&& raxmlHPC-PTHREADS -m GTRGAMMA   -n con.tre.tre -J MR -z RAxML_bootstrap.boot.tre
~


RAXMLHPC2_WORKFLOW
This test:
toolId=RAXMLHPC2_WORKFLOW_DRAFT
runtime_=0.50
select_workflow_=BOOTCON	       (no default)
choose_bootstop_=specify		   (this is default, can be "bootstop")
choose_bootstrap_=x                (set rapid bootstrapping, otherwise "b")
bootstrap_value=100			   (default = 100)
datatype_=dna                  (default, can be others)
dna_gtrcat_=GTRGAMMA           (no default, a value for the model must be set)
outgroup_=					   (default)
provide_parsimony_seed_=1	   (default)
parsimony_seed_val_=12345	   (default)
disable_seqcheck_=1            (sets the -O value, default is off)
outsuffix_BOOTCON_=boot		   (sets file name using -n, default = boot)
rapidbootstrap_seed_val=12345  (default)
outsuffix_BOOTCON2_=con. tre		   (sets output file name using -n step 2, default = con.tre)
rapidbootstrap_seed_val_=12345     (set the bootstrap seed, default 12345, so it isnt required to set it)

raxmlHPC-HYBRID (-T 16) -m GTRGAMMA   -n boot.tre -s infile.txt  -O  -x 12345  -N 100 -p 12345 
&& raxmlHPC-PTHREADS (-T 8) -m GTRGAMMA -n con.tre.tre -J MR -z RAxML_bootstrap.boot.tre'

test passed


other model options:
If not DNA , set datatype_=(protein/rna/binary/multi) then set this parameter
(GTRCAT default;  prot_sub_model_=PROTGAMMA/PROTCAT; rna_model_ ;bin_model_=BINCAT/BINGAMMA; multi_model_=MULTICAT/MULTIGAMMA)
Then set sub_parameters for protein:
prot_matrix_spec_= (DAYHOFF is default)

other modifiers can be set:
invariable_= - switch - Estimate proportion of invariable sites (GTRGAMMA + I)
ascertainment_= switch -
ascertainment_corr_= excl - sets the kind of correction used
use_emp_freqs_= to use empirical frequencies, protein only 

outgroup_ - String - Outgroup (one or more comma-separated outgroups, see comment for syntax)

upload modifying files
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)

printbrlength_ - Switch - Print branch lengths (-k)