set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$name_in' name_in.dat &&
ln -s '$group_in' group_in.dat &&
ln -s '$taxonomy_in' taxonomy_in.dat &&
#if $trim.method == "oligos":
    ln -s '$trim.oligos' trim.oligos.dat &&
#elif $trim.method == "reference":
    ln -s '$trim.ecoli' trim.ecoli.dat &&
#end if

echo 'pcr.seqs(
    fasta=fasta.dat,
    #if $name_in
        name=name_in.dat,
    #end if
    #if $group_in:
        group=group_in.dat,
    #end if
    #if $taxonomy_in:
        taxonomy=taxonomy_in.dat,
    #end if
    #if $trim.method == "oligos":
        oligos=trim.oligos.dat,
        nomatch=$trim.nomatch,
        $trim.keepprimer
    #elif $trim.method == "reference":
        ecoli=trim.ecoli.dat,
    #elif $trim.method == "position":
        start=$trim.start,
        #if $trim.end and int($trim.end) > 0:
            end=$trim.end,
        #end if
    #end if
    pdiffs=$pdiffs,
    rdiffs=$rdiffs,
    $keepdots
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log