qiime phylogeny iqtree-ultrafast-bootstrap

--i-alignment=$ialignment

#if str($pseed):
 --p-seed="$pseed"
#end if


#set $pncores = '${GALAXY_SLOTS:-4}'
#if str($pncores):
--p-n-cores=$pncores
#end if


#if str($pnruns):
 --p-n-runs=$pnruns
#end if

#if str($psubstitutionmodel) != 'None':
 --p-substitution-model=$psubstitutionmodel
#end if

#if str($pbootstrapreplicates):
 --p-bootstrap-replicates=$pbootstrapreplicates
#end if

#if str($pninitparstrees):
 --p-n-init-pars-trees="$pninitparstrees"
#end if

#if str($pntopinittrees):
 --p-n-top-init-trees="$pntopinittrees"
#end if

#if str($pnbestretaintrees):
 --p-n-best-retain-trees="$pnbestretaintrees"
#end if

#if str($pstopiter):
 --p-stop-iter="$pstopiter"
#end if

#if str($pperturbnnistrength):
 --p-perturb-nni-strength="$pperturbnnistrength"
#end if

#if str($psprradius):
 --p-spr-radius="$psprradius"
#end if

#if str($pnmaxufbootiter):
 --p-n-max-ufboot-iter="$pnmaxufbootiter"
#end if

#if str($pnufbootsteps):
 --p-n-ufboot-steps="$pnufbootsteps"
#end if

#if str($pmincorufboot):
 --p-min-cor-ufboot="$pmincorufboot"
#end if

#if str($pepbreakufboot):
 --p-ep-break-ufboot="$pepbreakufboot"
#end if

#if $pallnni:
 --p-allnni
#end if

#if str($palrt):
 --p-alrt="$palrt"
#end if

#if $pabayes:
 --p-abayes
#end if

#if str($plbp):
 --p-lbp="$plbp"
#end if

#if $pbnni:
 --p-bnni
#end if

#if $psafe:
 --p-safe
#end if

--o-tree=otree
;
cp otree.qza $otree