GalaxyGetOpt Quickstart
=======================

Use of `GalaxyGetOpt` is incredibly simple. This is partially a result
of it being rather unpythonic as I came from a Perl world.

.. code-block:: python

    #!/usr/bin/env python
    """
    Docstring goes here
    """
    from galaxygetopt.ggo import GalaxyGetOpt as GGO


    def main():
        c = GGO(
            options=[
                ['int', 'An integer parameter', {'required': True, 'validate':
                                                'Int', 'default': 10}],
                ['float', 'A float', {'required': True, 'validate': 'Float',
                                    'default': 1e-4}],
                ['string', 'A string value', {'required': True, 'multiple': True,
                                            'default': ['Hello', 'World'],
                                            'validate': 'String'}],
                [],
                ['Advanced'],
                ['option', 'A selection type parameter', {'required': False,
                                                        'validate': 'Option',
                                                        'options': {'a': 'Alpha',
                                                                    'b': 'Bravo'}
                                                        }],
                ['file', 'An input file', {'required': True, 'validate':
                                        'File/Input'}],
                ['tag', 'Genomic Tag', {'required': True, 'validate':
                                        'Genomic/Tag'}]
            ],
            outputs=[
                [
                    'test_output',
                    'Main output file of this utility',
                    {
                        'validate': 'File/Output',
                        'required': True,
                        'default': 'ggo_out.complex',
                        'data_format': 'text/tabular',
                        'default_format': 'TSV_U',
                    }
                ]
            ],
            defaults={
                'appid': 'ggo.testscript.complex',
                'appname': 'GGO Complex Test Script',
                'appdesc': 'tests functinoality of ggo',
                'appvers': '1.0.0',
            },
            tests=[
                {
                    'test_name': 'Default',
                    'params': {'tag': 'CDS'},
                    'outputs': {
                        'test_output': ['ggo_out.complex.Sheet1.tsv', 'galaxygetopt/tests/test_file.tsv'],
                    }
                }
            ],
            doc=__doc__
        )
        my_params = c.params()

This GGO invocation was originally incredibly simple, starting with
only `options`. Over time, the need for storing data like application
name and version was added, as was the code for `outputs`. Outputs
represent a file that will be written that is of interest to the user.
Included in `galaxygetopt` are several output handlers: output
formatters that take a specific internal data structure and produce
output formatted to whatever the user wants. In our Perl version of
this module, we provide output handlers for 

   - Spreadsheets: XLS, ODS
   - Flat tabular files: CSV, CSV (Unquoted), TSV, TSV (Unquoted)
   - Raw structures: YAML, JSON

This can be seen in the definition of an output structure (`data`) and
the call to `galaxygetopt.outputfiles.CRR` which writes the data to
disk

.. code-block:: python

    from galaxygetopt.outputfiles import OutputFiles
    of = OutputFiles(name='test_output', GGO=c)
    data = {
        'Sheet1': {
            'header': ['Key', 'Value'],
            'data': []
        }
    }
    tbl_data = []
    for key in my_params:
        tbl_data.append([key, my_params[key]])
    data['Sheet1']['data'] = tbl_data

    of.CRR(data=data)