#if str($input_type_cond.input_type) in ['single', 'pair']:
    #set read1 = $input_type_cond.read1
    ## bbmerge uses the file extension to determine the input format.
    #set ext = '.fastq'
    #if $read1.ext.endswith('.gz'):
        #set ext = $ext + '.gz'
    #end if
    #set read1_file = 'forward' + $ext
    ln -s '${read1}' '${read1_file}' &&
    #if str($input_type_cond.input_type) == 'pair':
        #set read2 = $input_type_cond.read2
        #set read2_file = 'reverse' + $ext
        ln -s '${read2}' '${read2_file}' &&
    #end if
#else:
    #set read1 = $input_type_cond.reads_collection['forward']
    ## bbmap uses the file extension to determine the input format.
    #set ext = '.fastq'
    #if $read1.ext.endswith('.gz'):
        #set ext = $ext + '.gz'
    #end if
    #set read1_file = 'forward' + $ext
    ln -s '${read1}' '${read1_file}' &&
    #set read2 = $input_type_cond.reads_collection['reverse']
    #set read2_file = 'reverse' + $ext
    ln -s '${read2}' '${read2_file}' &&
#end if

if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then
    export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m";
fi &&

bbmerge.sh tmpdir="\$TMPDIR" t="\${GALAXY_SLOTS:-2}"

#### Input parameters
#if str($input_type_cond.input_type) == 'single':
    in='${read1_file}'
    interleaved=t
#else:
    in1='${read1_file}' in2='${read2_file}'
    interleaved=f
#end if

#### Output options
out=merged.fastq
outu=unmerged.fastq
ihist=ihist.tabular
touppercase=t

#### Quality and trimming parameters
qtrim='$qt_options.qtrim'
trimq='$qt_options.trimq'
minlength='$qt_options.minlength_after_trim'
usequality='$qt_options.usequality'

#### Merging parameters
usejni=f ## Do overlapping in C code, which is faster.
ecco='$merge_options.ecco'
trimnonoverlapping='$merge_options.trimnonoverlapping'
mininsert='$merge_options.mininsert'
minoverlap='$merge_options.minoverlap'
minq='$merge_options.minq'
maxq='$merge_options.maxq'
entropy='$merge_options.entropy'
efilter='$merge_options.efilter'
pfilter='$merge_options.pfilter'
kfilter='$merge_options.kfilter'
usequality='$merge_options.usequality'

#if $merge_options.adapters.selector == "with_adaptors":
    adapter1='$merge_options.adapter1'
    adapter2='$merge_options.adapter2'
#end if

#if $merge_options.merge_mode.selector == 'Ratio mode':
    maxratio='$merge_options.merge_mode.maxratio'
    ratiomargin='$merge_options.merge_mode.ratiomargin'
    ratiooffset='$merge_options.merge_mode.ratiooffset'
    maxmismatches='$merge_options.merge_mode.maxmismatches'
    ratiominoverlapreduction=0
    minsecondratio='$merge_options.merge_mode.minsecondratio'
#else:
    margin='$merge_options.merge_mode.margin'
    mismatches='$merge_options.merge_mode.mismatches'
    requireratiomatch='$merge_options.merge_mode.requireratiomatch'
#end if

$merge_options.strictness=t