set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$fasta_in' fasta_in.dat &&
ln -s '$name_in' name_in.dat &&
ln -s '$count' count.dat &&
ln -s '$alignment.template' alignment.template.dat &&
#if $qual.use == "yes":
    ln -s '$qual.qfile_in' qfile_in.dat &&
    ln -s '$qual.alignreport_in' alignreport_in.dat &&
#end if

echo 'seq.error(
    fasta=fasta_in.dat,
    reference=alignment.template.dat,
    #if $name_in:
        name=name_in.dat,
    #end if
    #if $qual.use == "yes":
        qfile=qfile_in.dat,
        report=alignreport_in.dat,
    #end if
    #if $threshold:
        threshold=$threshold,
    #end if
    ignorechimeras=$ignorechimeras,
    #if $count:
        count=count.dat,
    #end if
    #if $fasta_in.is_of_type('mothur.align')
        aligned=T,
    #else
        aligned=F,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log