iqtree
    --prefix PREF
    #if $general_options.short_alignments:
        -T 1
    #else:
        -T \${GALAXY_SLOTS:-10}
    #end if
    --redo

## file
#if $general_options.s
    -s '$general_options.s'
#end if

#if $general_options.o
    -o '$general_options.o'
#end if
--seqtype $general_options.seqtype
## file
#if $general_options.t
    -t '$general_options.t'
    $tree_parameters.constructing_consensus.contree
    $tree_parameters.constructing_consensus.connet
    #if str($tree_parameters.constructing_consensus.burnin) != ''
        --burnin '$tree_parameters.constructing_consensus.burnin'
    #end if

    ## file
    #if $tree_parameters.constructing_consensus.support
        --support '$tree_parameters.constructing_consensus.support'
    #end if

    #if str($tree_parameters.constructing_consensus.suptag) != ''
        --suptag '$tree_parameters.constructing_consensus.suptag'
    #end if

    ## file
    #if $tree_parameters.computing_robinson_foulds.tree_dist_all
        $tree_parameters.computing_robinson_foulds.tree_dist_all
        --tree-dist $tree_parameters.computing_robinson_foulds.tree_dist
        --tree-dist2 $tree_parameters.computing_robinson_foulds.tree_dist2
    #end if
    $tree_parameters.ancestral_state.ancestral
    #if $tree_parameters.ancestral_state.asr_min:
        --asr-min $tree_parameters.ancestral_state.asr_min
    #end if
    #if $tree_parameters.concordance_factor.gcf:
        --gcf '$tree_parameters.concordance_factor.gcf'
    #end if
    #if $tree_parameters.concordance_factor.scf:
        --scf '$tree_parameters.concordance_factor.scf'
    #end if
    $tree_parameters.concordance_factor.df_tree
    $tree_parameters.concordance_factor.cf_verbose
    $tree_parameters.concordance_factor.cf_quartet
    $tree_parameters.symmetry_test.symtest
    $tree_parameters.symmetry_test.symtest_remove_bad
    $tree_parameters.symmetry_test.symtest_remove_good
    $tree_parameters.symmetry_test.symtest_keep_zero
    #if $tree_parameters.symmetry_test.symtest_pval:
        --symtest-pval $tree_parameters.symmetry_test.symtest_pval
    #end if
    #if $tree_parameters.symmetry_test.symtest_type:
        --symtest-type $tree_parameters.symmetry_test.symtest_type
    #end if
#end if

## date options
#if str($time_tree.date_source.select_source) == 'dataset':
    #if $time_tree.date_source.date:
        --date '$time_tree.date_source.date'
    #end if
#elif str($time_tree.date_source.select_source) == 'input':
    --date TAXNAME
    #if str($time_tree.date_source.date_tip) != '':
        --date-tip '$time_tree.date_source.date_tip'
    #end if
    #if str($time_tree.date_source.date_root) != '':
        --date-root '$time_tree.date_source.date_root'
    #end if
    #if str($time_tree.date_source.date_ci) != '':
        --date-ci '$time_tree.date_source.date_ci'
    #end if
    #if str($time_tree.date_source.clock_sd) != '':
        --clock-sd '$time_tree.date_source.clock_sd'
    #end if
    #if str($time_tree.date_source.date_outlier) != '':
        --date-outlier '$time_tree.date_source.date_outlier'
    #end if
    #if str($time_tree.date_source.date_options) != '':
        --date-options '$time_tree.date_source.date_options'
    #end if
    --dating LSD
    $time_tree.date_source.date_no_outgroup
#end if

## file
#if str($general_options.epsilon) != ''
    --epsilon '$general_options.epsilon'
#end if

#if str($general_options.seed) != ''
    --seed '$general_options.seed'
#end if

$general_options.keep_ident
$general_options.safe

#if str($likelihood_mapping.lmap) != ''
    --lmap '$likelihood_mapping.lmap'
#end if

## file
#if $likelihood_mapping.lmclust
    --lmclust '$likelihood_mapping.lmclust'
#end if

$likelihood_mapping.quartetlh

#if $modelling_parameters.automatic_model.cond_model.opt_custommodel:
    -m '$modelling_parameters.automatic_model.cond_model.m'
#else:
    #if str($modelling_parameters.automatic_model.cond_model.m) != ''
        #if $modelling_parameters.automatic_model.cond_model.additional_models:
            -m '$modelling_parameters.automatic_model.cond_model.m${$modelling_parameters.automatic_model.cond_model.additional_models}'
        #else:
            -m '$modelling_parameters.automatic_model.cond_model.m'
        #end if
    #end if
#end if

#if str($modelling_parameters.automatic_model.merge_strategy.merge) != 'none':
    --merge $modelling_parameters.automatic_model.merge_strategy.merge
    #if str($modelling_parameters.automatic_model.merge_strategy.merge) == 'rcluster':
        --rcluster $modelling_parameters.automatic_model.merge_strategy.rcluster
    #end if
    #if str($modelling_parameters.automatic_model.merge_strategy.merge) == 'rclusterf':
        --rclusterf $modelling_parameters.automatic_model.merge_strategy.rclusterf
    #end if
    #if str($modelling_parameters.automatic_model.merge_strategy.merge) in ['rcluster', 'rclusterf']:
        --rcluster-max $modelling_parameters.automatic_model.merge_strategy.rcluster_max
    #end if
#end if

#if str($modelling_parameters.automatic_model.mset) != ''
    --mset '$modelling_parameters.automatic_model.mset'
#end if

#if str($modelling_parameters.automatic_model.msub) != ''
    --msub '$modelling_parameters.automatic_model.msub'
#end if

#if str($modelling_parameters.automatic_model.mfreq) != ''
    --mfreq '$modelling_parameters.automatic_model.mfreq'
#end if

#if str($modelling_parameters.automatic_model.mrate) != ''
    --mrate '$modelling_parameters.automatic_model.mrate'
#end if

#if str($modelling_parameters.automatic_model.cmin) != ''
    --cmin '$modelling_parameters.automatic_model.cmin'
#end if

#if str($modelling_parameters.automatic_model.cmax) != ''
    --cmax '$modelling_parameters.automatic_model.cmax'
#end if

#if str($modelling_parameters.automatic_model.merit) != ''
    --merit '$modelling_parameters.automatic_model.merit'
#end if

$modelling_parameters.automatic_model.mtree

#if str($modelling_parameters.automatic_model.madd) != ''
    --madd '$modelling_parameters.automatic_model.madd'
#end if

## file
#if $modelling_parameters.automatic_model.mdef
    --mdef '$modelling_parameters.automatic_model.mdef'
#end if

$modelling_parameters.automatic_model.modelomatic
$modelling_parameters.specifying_substitution.mix_opt

#if str($modelling_parameters.rate_heterogeneity.alpha_min) != ''
    --alpha-min '$modelling_parameters.rate_heterogeneity.alpha_min'
#end if

$modelling_parameters.rate_heterogeneity.gamma_median

#if str($modelling_parameters.rate_heterogeneity.i) != ''
    -i '$modelling_parameters.rate_heterogeneity.i'
#end if

$modelling_parameters.rate_heterogeneity.opt_gamma_inv
$modelling_parameters.rate_heterogeneity.rate

#if str($modelling_parameters.partition_model.model_selection.model) != 'none':
    -$modelling_parameters.partition_model.model_selection.model '$modelling_parameters.partition_model.model_selection.model_file'
    #if str($modelling_parameters.partition_model.model_selection.subsample) != '':
        --subsample $modelling_parameters.partition_model.model_selection.subsample
    #end if
    #if str($modelling_parameters.partition_model.model_selection.subsample_seed) != '':
        --subsample-seed $modelling_parameters.partition_model.model_selection.subsample_seed
    #end if
#end if

## file
#if $modelling_parameters.site_specific_frequency.tree_freq
    --tree-freq '$modelling_parameters.site_specific_frequency.tree_freq'
#end if

#if str($modelling_parameters.site_specific_frequency.site_freq) != ''
    --site-freq '$modelling_parameters.site_specific_frequency.site_freq'
#end if

$modelling_parameters.site_specific_frequency.freq_max

#if str($tree_parameters.tree_search.ninit) != ''
    --ninit '$tree_parameters.tree_search.ninit'
#end if

#if str($tree_parameters.tree_search.ntop) != ''
    --ntop '$tree_parameters.tree_search.ntop'
#end if

#if str($tree_parameters.tree_search.nbest) != ''
    --nbest '$tree_parameters.tree_search.nbest'
#end if

#if str($tree_parameters.tree_search.nstop) != ''
    --nstop '$tree_parameters.tree_search.nstop'
#end if

#if str($tree_parameters.tree_search.n) != ''
    -n '$tree_parameters.tree_search.n'
#end if

#if str($tree_parameters.tree_search.radius) != ''
    --radius '$tree_parameters.tree_search.radius'
#end if

#if str($tree_parameters.tree_search.perturb) != ''
    --perturb '$tree_parameters.tree_search.perturb'
#end if

$tree_parameters.tree_search.allnni
$tree_parameters.tree_search.tree_fix
$tree_parameters.tree_search.fast
$tree_parameters.tree_search.polytomy
$tree_parameters.tree_search.treels
$tree_parameters.tree_search.show_lh
$tree_parameters.tree_search.terrace

## file
#if $tree_parameters.tree_search.g
    -g '$tree_parameters.tree_search.g'
#end if

#if str($tree_parameters.single_branch.alrt) != ''
    --alrt '$tree_parameters.single_branch.alrt'
#end if

$tree_parameters.single_branch.abayes

#if str($tree_parameters.single_branch.lbp) != ''
    --lbp '$tree_parameters.single_branch.lbp'
#end if

## file
#if $tree_parameters.tree_topology.trees
    --trees '$tree_parameters.tree_topology.trees'
#end if

#if str($tree_parameters.tree_topology.test) != ''
    --test '$tree_parameters.tree_topology.test'
#end if

$tree_parameters.tree_topology.test_weight
$tree_parameters.tree_topology.test_au

#if str($tree_parameters.constructing_consensus.sup_min) != ''
    --sup-min '$tree_parameters.constructing_consensus.sup_min'
#end if


#if str($tree_parameters.generating_random.r) != ''
    -r '$tree_parameters.generating_random.r'
#end if

#if $tree_parameters.generating_random.rand
    $tree_parameters.generating_random.rand
#end if

#if str($tree_parameters.generating_random.branch_min) != '' and str($tree_parameters.generating_random.branch_mean) != '' and str($tree_parameters.generating_random.branch_max) != ''
    --rlen $tree_parameters.generating_random.branch_min $tree_parameters.generating_random.branch_mean $tree_parameters.generating_random.branch_max
#end if

#if str($bootstrap_parameters.ultrafast_bootstrap.ufboot) != ''
    --ufboot '$bootstrap_parameters.ultrafast_bootstrap.ufboot'
#end if

#if str($bootstrap_parameters.ultrafast_bootstrap.ufjack) != ''
    --ufjack '$bootstrap_parameters.ultrafast_bootstrap.ufjack'
#end if

#if str($bootstrap_parameters.ultrafast_bootstrap.jack_prop) != ''
    --jack-prop '$bootstrap_parameters.ultrafast_bootstrap.jack_prop'
#end if

#if str($bootstrap_parameters.ultrafast_bootstrap.sampling) != ''
    --sampling '$bootstrap_parameters.ultrafast_bootstrap.sampling'
#end if

$bootstrap_parameters.ultrafast_bootstrap.boot_trees
$bootstrap_parameters.ultrafast_bootstrap.wbtl

#if str($bootstrap_parameters.ultrafast_bootstrap.nmax) != ''
    --nmax '$bootstrap_parameters.ultrafast_bootstrap.nmax'
#end if

#if str($bootstrap_parameters.ultrafast_bootstrap.nstep) != ''
    --nstep '$bootstrap_parameters.ultrafast_bootstrap.nstep'
#end if

#if str($bootstrap_parameters.ultrafast_bootstrap.bcor) != ''
    --bcor '$bootstrap_parameters.ultrafast_bootstrap.bcor'
#end if

#if str($bootstrap_parameters.ultrafast_bootstrap.beps) != ''
    --beps '$bootstrap_parameters.ultrafast_bootstrap.beps'
#end if

$bootstrap_parameters.ultrafast_bootstrap.bnni

#if str($bootstrap_parameters.nonparametric_bootstrap.boot) != ''
    --boot '$bootstrap_parameters.nonparametric_bootstrap.boot'
#end if

#if str($bootstrap_parameters.nonparametric_bootstrap.jack) != ''
    --jack '$bootstrap_parameters.nonparametric_bootstrap.jack'
#end if

#if str($bootstrap_parameters.nonparametric_bootstrap.jack_prop) != ''
    --jack-prop '$bootstrap_parameters.nonparametric_bootstrap.jack_prop'
#end if

$bootstrap_parameters.nonparametric_bootstrap.bcon
$bootstrap_parameters.nonparametric_bootstrap.bonly
$bootstrap_parameters.nonparametric_bootstrap.tbe

#if str($miscellaneous_options.fconst) != ''
    --fconst '$miscellaneous_options.fconst'
#end if