set -o pipefail; export TERM=vt100; 

## enable mothur to find blast
ln -s `dirname \$(which mothur)`/* . &&

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$alignment.template' alignment.template.dat &&
ln -s '$tax.taxonomy' tax.taxonomy.dat &&
ln -s '$count' count.dat &&
ln -s '$name' name.dat &&

echo 'classify.seqs(
    fasta=fasta.dat,
    reference=alignment.template.dat,
    taxonomy=tax.taxonomy.dat,
    method=$classify.method,
    #if $classify.method == "wang":
        ksize=$classify.ksize,
        iters=$classify.iters,
        cutoff=$classify.cutoff,
        probs=$classify.probs,
    #elif $classify.method == "knn":
        numwanted=$classify.numwanted,
        search=$classify.search.algorithm,
        #if $classify.search.algorithm == "kmer":
            ksize=$classify.search.ksize,
        #elif $classify.search.algorithm == "blast":
            match=$classify.search.match,
            mismatch=$classify.search.mismatch,
            gapopen=$classify.search.gapopen,
            gapextend=$classify.search.gapextend,
        #end if
    #end if
    #if $count:
        count=count.dat,
    #end if
    #if $name:
        name=name.dat,
    #end if
    relabund=$relabund,
    output=$output,
    printlevel=$printlevel,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| ./mothur
| tee mothur.out.log