new_contents: #!/usr/bin/env python
  """Module to generically wrap modules for usage from within Galaxy.
  First command line argument is a module, e.g: "translate".
  Second command line argument is a file to log any output to.
  Further arguments are passed to the named module's main method."""
  
  __author__ = "Tim te Beek"
  __contact__ = "brs@nbic.nl"
  __copyright__ = "Copyright 2011, Netherlands Bioinformatics Centre"
  __license__ = "MIT"
  
  # First argument contains fully qualified name of module to be imported
  import logging
  import sys
  NAME = sys.argv[1]
  try:
      MODULE = __import__(NAME)
  except ImportError as ie:
      print('Could not import {0}'.format(NAME))
      raise
  
  # Second argument contains name of logging output file to use
  FILE_HANDLER = logging.FileHandler(sys.argv[2], mode='w')
  FILE_HANDLER.setFormatter(logging.Formatter())
  FILE_HANDLER.setLevel(logging.INFO)
  logging.root.addHandler(FILE_HANDLER)
  
  try:
      # Run main method within module with remaining arguments
      if sys.argv[3:]:
          MODULE.main(sys.argv[3:])
      else:
          MODULE.main()
  except SystemExit:
      # Do not report SystemExit errors to FogBugz: Just exit
      raise
  except AssertionError:
      # Do not report AssertionErrors to FogBugz: Not a bug we care about
      logging.exception('An assumption failed')
      raise
  except:
      # Should any other error occur, report it to FogBugz automatically
      # TODO from bugzscout import report_error_to_email
      #MESSAGE = report_error_to_email()
      #logging.info('Automatic bug submission reported: %s', MESSAGE)
      logging.exception('An error occurred')
      raise
  finally:
      # Always remove logging handler from root
      logging.root.removeHandler(FILE_HANDLER)
  
  # Snippet to log available environment variables from inside a Galaxy tool:
  # for key in sorted($searchList[2].keys())
  # silent   sys.stderr.write("\t{0} = {1} ({2})\n".format(str(key), str($searchList[2][key]), type($searchList[2][key])))
  # end for
  
subject: Add wrapper.py here so imports will work when all is symlinked in /tools