#import re
#import os

#if $input.type == 'fasta'
#set $input_files = '"{}.fasta"'.format(os.path.splitext($input.fasta.name)[0])
  ln -s "$input.fasta" $input_files &&
#elif $input.type == 'paired'
#set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.forward.name) else '.fastq'
#set $_forward = '"{}_1{}"'.format($re.sub(r'_[12]\..+$', '', $input.forward.name), $_forward_ext)
#set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.reverse.name) else '.fastq'
#set $_reverse = '"{}_2{}"'.format($re.sub(r'_[12]\..+$', '', $input.reverse.name), $_reverse_ext)
#set $input_files = '{} {}'.format($_forward, $_reverse)
  ln -s "$input.forward" $_forward &&
  ln -s "$input.reverse" $_reverse &&
#elif $input.type == 'single'
#set $input_files = '"{}"'.format($input.single.name)
  ln -s "$input.single" $input_files &&
#elif $input.type == 'paired_collection'
#set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', str($input.paired_collection.forward)) else '.fastq'
#set $_forward = '"{}_1{}"'.format($input.paired_collection.name, $_forward_ext)
#set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', str($input.paired_collection.reverse)) else '.fastq'
#set $_reverse = '"{}_2{}"'.format($input.paired_collection.name, $_reverse_ext)
#set $input_files = '{} {}'.format($_forward, $_reverse)
  ln -s "$input.paired_collection.forward" $_forward &&
  ln -s "$input.paired_collection.reverse" $_reverse &&
#end if

refseq_masher
  $adv.verbosity
  contains
  --output refseq_masher-contains.${adv.output_type}
  --output-type $adv.output_type
  --top-n-results $adv.top_n_results
  --parallelism "\${GALAXY_SLOTS:-1}"
  --min-identity $adv.min_identity
  --max-pvalue $adv.max_pvalue
  $input_files