set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
#if $template.source == "self":
    ln -s '$template.count' template.count.dat &&
    ln -s '$template.group' template.group.dat &&
#elif $template.source == "names":
    ln -s '$template.name' template.name.dat &&
#else:
    ln -s '$template.reference' template.reference.dat &&
#end if

echo 'chimera.uchime(
    fasta=fasta.dat,
    #if $template.source == "self":
        reference=self,
        #if float($template.abskew) > 0:
            abskew=$template.abskew,
        #end if
        #if $template.group:
            group=template.group.dat,
        #end if
        #if $template.count:
            count=template.count.dat,
        #end if
    #elif $template.source == "names":
        name=template.name.dat,
    #else:
        reference=template.reference.dat,
    #end if
    minh=$minh,
    mindiv=$mindiv,
    xn=$xn,
    dn=$dn,
    xa=$xa,
    chunks=$chunks,
    minchunk=$minchunk,
    #if $idsmoothwindow:
        idsmoothwindow=$idsmoothwindow,
    #end if
    maxp=$maxp,
    minlen=$minlen,
    maxlen=$maxlen,
    skipgaps=$skipgaps,
    skipgaps2=$skipgaps2,
    #if $alignment.ucl == "local":
        ucl=true,
        #if $alignment.queryfract:
            queryfract=$alignment.queryfract,
        #end if
    #end if
    dereplicate=$dereplicate,
    chimealns=$chimealns,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
2>&1  ## uchime component writes output to stderr