Module Documentation

The GalaxyGetOpt class is

class galaxygetopt.ggo.GalaxyGetOpt(options=, []outputs=, []defaults={}, tests=, []doc=None, argv=None)

convert_opt_arr_to_params(options_array, outputs)

Returns a completed parameterCollection object

Internally we add a couple other parameters that should be available to the user to our parameterCollection. Inside PC the “verbose” option is added, while here we add:

• generate_galaxy_xml
• galaxy
• outfile_supporting

The outfile_supporting variable is used as the location to place generated files (primary_NNNN_blah_visible_txt)

fix_outputs(outputs)

Internal function to parse specified outputs and munge them into standard options

From a user perspective, they only specify a single output file and it is supposed to be handled magically. This function is a significant part of that magic.

Internally, an output file is taken from being a simple object to four separate command line parameters, completely removed from the original description of the option. These four parameters are as follows for an example output file “of”:

• of: the file location as specified by the user (if specified at all, without extension)
• of_format: the format of this file. Really only applies to the top level file, but it’s up to the dev how to handle this value
• of_files_path: the “of.files_path” value in the cheetah template galaxy uses. This location can be used for storing images or other data for use in HTML files.
• of_id: the “of.id” value in the cheetah template, used in generation of the complex filenames that galaxy requires to pick up on associated files.

There should be no need for the user to call this method.

params()

Returns parameters, or prints help and exits if validation fails

serialize_opt_to_yaml(options=, []outputs=, []defaults={}, tests=[])

Dumps options interface to yaml