set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
#if $groupnames.source == "other":
    ln -s '$groupnames.group_in' groupnames_group_in.dat &&
    ln -s '$groupnames.fasta_in' groupnames_fasta_in.dat &&
    ln -s '$groupnames.name_in' groupnames_name_in.dat &&
    ln -s '$groupnames.list_in' groupnames_list_in.dat &&
    ln -s '$groupnames.taxonomy_in' groupnames_taxonomy_in.dat &&
    ln -s '$groupnames.column_in' groupnames_column_in.dat &&
    ln -s '$groupnames.phylip_in' groupnames_phylip_in.dat &&
#else
    ln -s '$groupnames.shared_in' groupnames_shared_in.dat &&
#end if

echo 'remove.groups(
    #if $groupnames.source == "other":
        #if $group_in.is_of_type("mothur.groups"):
            group=groupnames_group_in.dat
        #else
            count=groupnames_group_in.dat
        #end if
        #if $groupnames.fasta_in:
            ,fasta=groupnames_fasta_in.dat
        #end if
        #if $groupnames.name_in:
            ,name=groupnames_name_in.dat
        #end if
        #if $groupnames.list_in:
            ,list=groupnames_list_in.dat
        #end if
        #if $groupnames.taxonomy_in:
            ,taxonomy=groupnames_taxonomy_in.dat
        #end if
        #if $column_in:
            ,column=groupnames_column_in.dat
        #end if
        #if $phylip_in:
            ,phylip=groupnames_phylip_in.dat
        #end if
    #else
        shared=groupnames_shared_in.dat
    #end if
    ,groups=${ str($groupnames.groups).replace(",","-") }
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log