set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$names' names.dat &&
ln -s '$count' count.dat &&
#if $oligo.add == "yes":
    ln -s '$oligo.oligos' oligo.oligos.dat &&
#end if
#if $qual.add2 == "yes":
    ln -s '$qual.qfile' qual.qfile.dat &&
#end if

echo 'trim.seqs(
    fasta=fasta.dat,
    minlength=$minlength,
    maxlength=$maxlength,
    maxambig=$maxambig,
    maxhomop=$maxhomop,
    keepfirst=$keepfirst,
    removelast=$removelast,
    #if $oligo.add == "yes":
        oligos=oligo.oligos.dat,
        bdiffs=$oligo.bdiffs,
        pdiffs=$oligo.pdiffs,
        tdiffs=$oligo.tdiffs,
        ldiffs=$oligo.ldiffs,
        sdiffs=$oligo.sdiffs,
        keepforward=$oligo.keepforward,
        allfiles=$oligo.allfiles,
    #end if
    #if $qual.add2 == "yes":
        qfile=qual.qfile.dat,
        qaverage=$qual.qaverage,
        qthreshold=$qual.qthreshold,
        qwindowaverage=$qual.qwindowaverage,
        qwindowsize=$qual.qwindowsize,
        rollaverage=$qual.rollaverage,
        qstepsize=$qual.qstepsize,
        qtrim=$qual.qtrim,
    #end if
    flip=$flip,
    #if $names:
        name=names.dat,
    #end if
    logtransform=$logtransform,
    checkorient=$checkorient,
    #if $count:
        count=count.dat,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log

## prevent these two files from being gathered into collection
&& mv fasta.trim.fasta fasta.trim
&& mv fasta.scrap.fasta fasta.scrap