A template that can be used as I work on QIIME issue #774: https://github.com/qiime/qiime/issues/774

template_cl_interface.py

#!/usr/bin/env python
from __future__ import division

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2013, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.6.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "[email protected]"
__status__ = "Development"

from qiime.command import (WorkflowCommand, QiimeCommand)

qiime_config = load_qiime_config()
options_lookup = get_options_lookup()

class ScriptNameInCamelCase(WorkflowCommand):
    """
    """
    _brief_description = """"""
    _script_description = """"""
    _script_usage = []
    _script_usage_output_to_remove = []
    _output_description = """"""
    _required_options = []
    _optional_options = []
    _version = __version__
    
    _input_file_parameter_ids = []

    def run_command(self, 
                    options,
                    arguments):

        # create local copies of options
        verbose = options['verbose']
        
        # paste main() block from existing script