old_contents: """
  Usage:
      biobox short_read_assembler <image> [options]
  
  Options:
    -h, --help              Show this screen.
    -v, --version           Show version.
    -i FILE, --input=FILE   Source FASTQ file containing paired short reads
    -o FILE, --output=FILE  Destination FASTA file for assembled contigs
  
  """
  
  import biobox_cli.container   as ctn
  import biobox_cli.util        as util
  import biobox_cli.biobox_file as fle
  import os
  import tempfile as tmp
  
  def run(argv):
      opts  = util.command_line_args(__doc__, argv, False)
  
      image      = opts['<image>']
      fastq_file = opts['--input']
  
      if not ctn.image_available(image):
          msg = "No Docker image available with the name: {}"
          util.err_exit(msg.format(image))
  
      cntr_src_dir = "/fastq"
      cntr_dst_dir = "/assembly"
  
      host_src_dir = os.path.dirname(fastq_file)
      host_dst_dir = tmp.mkdtemp()
  
      biobox_args = fle.fastq_arguments(cntr_src_dir, [fastq_file, "paired"])
      biobox_path = fle.create_biobox_directory(fle.generate(biobox_args))
  
new_contents: """
  Usage:
      biobox short_read_assembler <image> [options]
  
  Options:
    -h, --help              Show this screen.
    -v, --version           Show version.
    -i FILE, --input=FILE   Source FASTQ file containing paired short reads
    -o FILE, --output=FILE  Destination FASTA file for assembled contigs
  
  """
  
  import biobox_cli.container   as ctn
  import biobox_cli.util        as util
  import biobox_cli.biobox_file as fle
  import os
  import tempfile as tmp
  
  def run(argv):
      opts  = util.command_line_args(__doc__, argv, False)
  
      image      = opts['<image>']
      fastq_file = opts['--input']
      biobox_args = fle.fastq_arguments(cntr_src_dir, [fastq_file, "paired"])
  
      if not ctn.image_available(image):
          msg = "No Docker image available with the name: {}"
          util.err_exit(msg.format(image))
  
      host_src_dir = os.path.dirname(fastq_file)
      host_dst_dir = tmp.mkdtemp()
      host_yml_dir = fle.create_biobox_directory(fle.generate(biobox_args))
  
      cntr_src_dir = "/fastq"
      cntr_dst_dir = "/assembly"
      cntr_yml_dir = "/bbx/input"
  
subject: Create arguments for container