set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$group_in' group_in.dat &&
ln -s '$fasta_in' fasta_in.dat &&
ln -s '$name_in' name_in.dat &&
ln -s '$list_in' list_in.dat &&
ln -s '$shared_in' shared_in.dat &&
ln -s '$taxonomy_in' taxonomy_in.dat &&
ln -s '$design_in' design_in.dat &&
ln -s '$column_in' column_in.dat &&
ln -s '$phylip_in' phylip_in.dat &&
#if $groupnames.source == 'accnos':
    ln -s '$groupnames.accnos' groupnames.accnos.dat &&
#end if

echo 'get.groups(
    #if $group_in.is_of_type("mothur.groups"):
        group=group_in.dat
    #else
        count=group_in.dat
    #end if
    #if $groupnames.source == 'groups':
        #if $groupnames.groups:
            ,groups=${ str($groupnames.groups).replace(",","-") }
        #end if
    #else
        ,accnos=groupnames.accnos.dat
    #end if
    #if $fasta_in:
        ,fasta=fasta_in.dat
    #end if
    #if $name_in:
        ,name=name_in.dat
    #end if
    #if $list_in:
        ,list=list_in.dat
    #end if
    #if $shared_in:
        ,shared=shared_in.dat
    #end if
    #if $taxonomy_in:
        ,taxonomy=taxonomy_in.dat
    #end if
    #if $design_in:
        ,design=design_in.dat
    #end if
    #if $column_in:
        ,column=column_in.dat
    #end if
    #if $phylip_in:
        ,phylip=phylip_in.dat
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log