set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$accnos' accnos.dat &&
ln -s '$fasta_in' fasta_in.dat &&
ln -s '$fastq_in' fastq_in.dat &&
ln -s '$count_in' count_in.dat &&
ln -s '$qfile_in' qfile_in.dat &&
ln -s '$name_in' name_in.dat &&
ln -s '$group_in' group_in.dat &&
ln -s '$alignreport_in' alignreport_in.dat &&
ln -s '$list_in' list_in.dat &&
ln -s '$taxonomy_in' taxonomy_in.dat &&

echo 'get.seqs(
    accnos=accnos.dat,
    #if $fasta_in:
        fasta=fasta_in.dat,
    #end if
    #if $fastq_in:
        fastq=fastq_in.dat,
    #end if
    #if $count_in:
        count=count_in.dat,
    #end if
    #if $qfile_in:
        qfile=qfile_in.dat,
    #end if
    #if $name_in:
        name=name_in.dat,
    #end if
    #if $group_in:
        group=group_in.dat,
    #end if
    #if $alignreport_in:
        alignreport=alignreport_in.dat,
    #end if
    #if $list_in:
        list=list_in.dat,
    #end if
    #if $taxonomy_in:
        taxonomy=taxonomy_in.dat,
    #end if
    dups=$dups
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log