set -o pipefail; export TERM=vt100; 

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

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

echo 'chimera.slayer(
    fasta=fasta.dat,
    #if $alignment.source == "self":
        reference=self,
        #if $alignment.name:
            name=$alignment.name,
        #end if
        #if $alignment.group:
            group=$alignment.group,
        #end if
        #if $alignment.count:
            count=$alignment.count,
        #end if
    #else:
        reference=$alignment.reference,
    #end if
    #if $options.setby == "user":
        search=$options.search,
        window=$options.window,
        increment=$options.increment,
        match=$options.match,
        mismatch=$options.mismatch,
        numwanted=$options.numwanted,
        parents=$options.parents,
        minsim=$options.minsim,
        mincov=$options.mincov,
        iters=$options.iters,
        minbs=$options.minbs,
        minsnp=$options.minsnp,
        divergence=$options.divergence,
        trim=$options.trim,
        split=$options.split,
    #end if
    dereplicate=$dereplicate,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| ./mothur
| tee mothur.out.log