old_contents: __author__ = "Behram Radmanesh"
  __copyright__ = "Copyright 2016, Behram Radmanesh"
  __email__ = "behram.radmanesh@nih.gov"
  __license__ = "MIT"
  
  # include any imports that will be needed, example below
  from snakemake.shell import shell
  
  # Use this block to support arbitrary arguments to be passed in to the shell
  # call without raising an error if no params.extra were provided. If there
  # aren't any additional params possible then you can delete this.
  try:
      extra = snakemake.params.extra
  except AttributeError:
      extra = ""
  
  # Use this block to redirect stdout and stderr to a log if it was provided.
  # Adjust the stdout/stderr redirection as needed.
  if snakemake.log:
      log = "> {} 2>&1".format(snakemake.log)
  else:
      log = ""
  
  # Formatting: put logical blocks of arguments together on one line, but use
  # multiple lines for clarity. Note the space at the end of each line for when
  # the lines are concatenated. Also note the use of {extra} and {log} as
  # specified above.
  shell(
      "featureCounts "
      "{extra} "
      "-a {snakemake.input.annoGTF} "
      "-o {snakemake.output.counts} "
      "{snakemake.input.mappingFile} "
      "{log} ")
  
new_contents: __author__ = "Behram Radmanesh"
  __copyright__ = "Copyright 2016, Behram Radmanesh"
  __email__ = "behram.radmanesh@nih.gov"
  __license__ = "MIT"
  
  # include any imports that will be needed, example below
  from snakemake.shell import shell
  
  # Use this block to support arbitrary arguments to be passed in to the shell
  # call without raising an error if no params.extra were provided. If there
  # aren't any additional params possible then you can delete this.
  try:
      extra = snakemake.params.extra
  except AttributeError:
      extra = ""
  
  # Use this block to redirect stdout and stderr to a log if it was provided.
  # Adjust the stdout/stderr redirection as needed.
  if snakemake.log:
      log = "> {} 2>&1".format(snakemake.log)
  else:
      log = ""
  
  # Formatting: put logical blocks of arguments together on one line, but use
  # multiple lines for clarity. Note the space at the end of each line for when
  # the lines are concatenated. Also note the use of {extra} and {log} as
  # specified above.
  shell(
      "featureCounts -T {snakemake.threads} "
      "{extra} "
      "-a {snakemake.input.annoGTF} "
      "-o {snakemake.output.counts} "
      "{snakemake.input.mappingFile} "
      "{log} ")
  
subject: fix threads in wrapper