toolId = IQTREE_XSEDE_EXPANSE

########################################
#               required values                                                            #
########################################
#runtime in hours; let the user set this, 0.1 through 168 hours
runtime_ = 168
# you might make it possible for user to specify,, but the default of 1000 is fine unless the data set might be >> 1000 patterns
specify_numpatterns_ 1000
#no default, the app must set this, it can always be set at 2 (tree inference only), or you can allow user to chose model test only (1)
specify_runtype_ = 2

#######################################
#           can allow user to provide these                                #
#######################################
#default=output,  user can set if you want to allow it
specify_prefix_ = iqtreeAnalysis
#default is NULL; user can set if you want to allow it, not required
specify_outgroup_ =charmander
###################################
#                                 other options                                  #
###################################
#by default, the program detects the data type
#the user can specify the sequence_type_ = BIN (allowed values are MORPH, BIN, DNA, AA; CODON, NT2AA)
#This can be useful, in case the program guesses wrong.
#THERE ARE THREE MODEL SPECIFICATION CHOICES. THEY ARE MUTAULLY EXCLUSIVE 
#preferred: let IQTree test and then decide what the best model for your data is; other values are allowed: TESTNEW; TESTMERGE; TESTNEWMERGE
specify_model_ =TEST
#the model selection option has three basic mutually exclusive choices: 
#specify_model_ allows IQ tree to decide the best model; 
#specify_binmodel_=  allows the user to choose; some users may want it.  Allowed values: JC2; GTR2; MK; ORDERED
#freetextmodel_ = allows the user to just enter the model freehand; for experienced users
#it might be useful to allow the user to enter their own model in free text. 

##################################
#         Bootstrapping                                                   #
#################################
#User may wish to do bootstrapping. This requires several additiona parameter.
#Invoke bootstrapping with 
#bootstrap_type_ = bb (Ultrafast); b (Non-Parametric; complete); bo (Non-Parametric; bo)bc (Non-Parametric; bc)
# When a value for bootstrap_type_ is chosen, you must also provide:
#num_bootreps_ and intger. At least 1000 when bootstrap_type_ = bb
# at least 100 recommended when bootstrap_type_ is used, but not equal to bb
#many other bootstrap options, but we cna explore those as needed.