#import os.path
#import re
#def symlink_basename($f, strip_ext=False):
    #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
    #if strip_ext:
        #if $fn.endswith('.gz'):
            #set $fn = $fn[:-3]
        #end if
        #if $f.ext.startswith('fasta'):
            #set $exts_to_drop = ('.fa', '.fasta', '.fna')
        #else:
            #set $exts_to_drop = []
        #end if
        #for $ext in $exts_to_drop:
            #if $fn.endswith($ext):
                #set $fn = $fn[:-len($ext)]
                #break
            #end if
        #end for
    #end if
${fn}#slurp
#end def

mkdir input
&&
#if $inputs.paired_or_single == 'single':
    #for $f in $inputs.input:
        ln -s '$f' 'input/${symlink_basename($f)}' &&
    #end for
#else:
    #for $f in $inputs.pair_input:
        ln -s '$f.forward' 'input/${symlink_basename($f.forward.dataset)}' &&
        ln -s '$f.reverse' 'input/${symlink_basename($f.reverse.dataset)}' &&
    #end for
#end if

#if $aligner_cond.taxAligner not in ('0', '3') and $aligner_cond.refDB_cond.refDB == 'history':
    #set $ext = $aligner_cond.refDB_cond.ref_fasta.ext
    #set $ref_fasta_symlink = $symlink_basename($aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + '.' + $ext
    ln -s '$aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
#end if

#if not $map:
    cat '$generated_mapping' &&
    #set map = $generated_mapping
#end if

set +e &&

lotus2
-i input/
-o output
-tmpDir tmp_folder
-threads "\${GALAXY_SLOTS:-1}"
-map '$map'
#if $other_opts.sdmopt:
    -sdmopt '$other_opts.sdmopt'
#end if
#if $other_opts.platform != '':
    -platform $other_opts.platform
#end if
#if $other_opts.barcode:
    -barcode '$other_opts.barcode'
#end if
#if $forwardPrimer:
    -forwardPrimer '$forwardPrimer'
#end if
#if $reversePrimer:
    -reversePrimer '$reversePrimer'
#end if
#if $other_opts.offtarget_cond.offtargetDB != 'no':
    -offtargetDB '$other_opts.offtarget_cond.ref_file'
#end if
-useMini4map $other_opts.useMini4map

-clustering $clu_cond.clustering
#if $clu_cond.clustering in ('1', '3'):
    #if str($clu_cond.id):
        -id $clu_cond.id
    #end if
#elif $clu_cond.clustering == '2':
    #if str($clu_cond.swarm_distance):
        -swarm_distance $clu_cond.swarm_distance
    #end if
#end if
#if $clu_args.derepMin:
    -derepMin '$clu_args.derepMin'
#end if

#if $clu_args.deactivateChimeraCheck != '':
    -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
#end if
#if str($clu_args.chim_skew):
    -chim_skew $clu_args.chim_skew
#end if

-taxAligner $aligner_cond.taxAligner
#if $aligner_cond.taxAligner == '0':
    #if str($aligner_cond.rdp_thr):
        -rdp_thr $aligner_cond.rdp_thr
    #end if
#elif $aligner_cond.taxAligner == '3':
    #if str($aligner_cond.utax_thr):
        -utax_thr $aligner_cond.utax_thr
    #end if
#else:
    #if $aligner_cond.refDB_cond.refDB == 'cached':
        #if $aligner_cond.refDB_cond.ref_db != '':
            -refDB $aligner_cond.refDB_cond.ref_db
            -greengenesSpecies $aligner_cond.refDB_cond.greengenesSpecies
        #end if
    #else:
        -refDB '$ref_fasta_symlink'
        -tax4refDB '$aligner_cond.refDB_cond.tax4refDB'
    #end if
    -useBestBlastHitOnly $aligner_cond.useBestBlastHitOnly
#end if
#if $tax_args.amplicon_cond.amplicon_type != '':
    -amplicon_type $tax_args.amplicon_cond.amplicon_type
#end if
#if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'):
    -ITSx $tax_args.amplicon_cond.ITSx
#end if

#if $tax_args.tax_group != '':
    -tax_group $tax_args.tax_group
#end if
-keepUnclassified $tax_args.keepUnclassified
#if str($tax_args.LCA_cover):
    -LCA_cover $tax_args.LCA_cover
#end if
#if str($tax_args.LCA_frac):
    -LCA_frac $tax_args.LCA_frac
#end if
-lulu $tax_args.lulu
-buildPhylo $tax_args.buildPhylo
#if $tax_args.taxExcludeGrep:
    -taxExcludeGrep '$tax_args.taxExcludeGrep'
#end if
; EXIT_VALUE=\$? ;

zip -8 -r -v output.zip output/
&&
exit \$EXIT_VALUE