toolId = IQTREE_XSEDE_EXPANSE
#in hours; let the user set this, 0.1 through 168 hours
runtime_ = 168
#required, user must set; user should select bin or multi; for mixed data sets, a partition file is required
#sequence_type_ = MORPH
#required, possible for user to select, but the default of 1000 is fine unless the data set might be >> 1000 patterns
specify_numpatterns_ 1000
#no default, required, you need to set this, it can always be 2 (tree inference only), or you can allow user to chose model test only (1)
specify_runtype_ = 2
#default=output, so it is not required but user can set if you want to allow it
specify_prefix_ = iqtreemorph
#default is NULL; user can set if you want to allow it, not required
specify_outgroup_ =charmander
#let IQTree test and then decide what the best model for your data is; other values are allowed: TESTNEW; TESTMERGE; TESTNEWMERGE
specify_model_ =TESTMERGE
###################################
#                                 other options                                  #
###################################
#the model selection option has three basic mutually exclusive choices: model_selection allows IQ tree to decide the best model; specify_binmodel allows the user to choose; freetextmodel_
#allows the user to just enter the model
#THESE CHOICES ARE MUTAULLY EXCLUSIVE 
#specify_binmodel_ can be set when model_selection_ = TEST; is not used; some users may want it.  Allowed values: JC2; GTR2; MK; ORDERED
#specify_binmodel_ =JC2
#it might be useful to allow the user to enter their own model in free text. 
#the parameter is: freetextmodel_ =<whatever the user enters>
##################################
#         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.