"sorted_by_DOB"), ("Compare two coordinate files", "To draw replicates of the same samples " "like for a procustes plot.", "%prog -i compare -m Fasting_Map.txt " "--compare_plots -o comparison") ] script_info['output_description']= "This script creates an output directory "+\ "with an HTML formated file named 'index.html' and a complementary "+\ "folder named 'emperor_required_resources'. Opening index.html with "+\ "Google's Chrome web browser will display a three dimensional "+\ "visualization of the processed PCoA data file and the corresponding "+\ "metadata mapping file." script_info['required_options'] = [ make_option('-i','--input_coords',type="existing_path",help='Depending on ' 'the plot to be generated, can be one of the following: (1) Filepath of ' 'a coordinates file to create a PCoA plot. (2) Directory path to a folder ' 'containing coordinates files to create a jackknifed PCoA plot. (3) ' 'Directory path to a folder containing coordinates files to compare the ' 'coordinates there contained when --compare_plots is enabled (useful ' 'for procustes analysis plots). For directories: hidden files, sub-' 'directories and files suffixed as \'_procrustes_results.txt\''), make_option('-m','--map_fp',type="existing_filepath",help='path to a ' 'metadata mapping file') ] script_info['optional_options'] = [ make_option('--number_of_axes', type=int, help='Number of axes to be ' 'incorporated in the plot. Only 3 will be displayed at any given time but ' 'this option modifies how many axes you can use for your visualization. ' 'Note that Emperor will only use the axes that explain more than 0.5% (this' ' will be shown as 1% in the GUI)of the variability [default: %default]', default=10), make_option('-a', '--custom_axes', type='string', help='Comma-separated ' 'list of metadata categories to use as custom axes in the plot. For '
__license__ = "BSD" __version__ = "0.9.3-dev" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "*****@*****.**" __status__ = "Development" script_info = {} script_info['brief_description'] = "" script_info['script_description'] = "" script_info['script_usage'] = [("", "", "")] script_info['output_description'] = "" script_info['required_options'] = [] script_info['optional_options'] = [ make_option('--suppress_unit_tests', action='store_true', help='suppress ' ' execution of Emperor\'s unit tests [default: %default]', default=False), make_option( '--suppress_script_usage_tests', action='store_true', help='suppress Emperor\'s script usage tests [default: %default]', default=False), make_option('--unittest_glob', help='wildcard pattern to match the unit ' 'tests to execute [default: %default]', default=None), make_option('--script_usage_tests', help='comma-separated list of the ' 'script usage tests to execute [default: run all]', default=None),
"Yoshiki Vazquez-Baeza"] #remember to add yourself if you make changes __license__ = "BSD" __version__ = "0.9.3-dev" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "*****@*****.**" __status__ = "Development" script_info = {} script_info['brief_description'] = "" script_info['script_description'] = "" script_info['script_usage'] = [("","","")] script_info['output_description']= "" script_info['required_options'] = [] script_info['optional_options'] = [ make_option('--suppress_unit_tests', action='store_true', help='suppress ' ' execution of Emperor\'s unit tests [default: %default]', default=False), make_option('--suppress_script_usage_tests', action='store_true', help= 'suppress Emperor\'s script usage tests [default: %default]',default=False), make_option('--suppress_javascript_unit_tests', action='store_true', help= 'suppress Emperor\'s JavaScript unit tests [default: %default]', default=False), make_option('--unittest_glob', help='wildcard pattern to match the unit ' 'tests to execute [default: %default]', default=None), make_option('--script_usage_tests', help='comma-separated list of the ' 'script usage tests to execute [default: run all]', default=None), make_option('-p', '--temp_filepath', type='existing_path', help='temporary ' 'directory where the script usage tests will be executed', default='/tmp/'), make_option('--emperor_scripts_dir', help='filepath where the scripts are' ' stored', type='existing_path', default=None) ] script_info['version'] = __version__
] script_info['output_description'] = \ ("This script creates an output directory with an HTML formated file " "named 'index.html' and a complementary folder named " "'emperor_required_resources'. Opening index.html with Google's Chrome " "web browser will display a three dimensional visualization of the " "processed PCoA data file and the corresponding metadata mapping file.") script_info['required_options'] = [ make_option('-i', '--input_coords', type="existing_path", help=("Depending on the plot to be generated, can be one of " "the following: (1) Filepath of a coordinates file to " "create a PCoA plot. (2) Directory path to a folder " "containing coordinates files to create a jackknifed " "PCoA plot. (3) Directory path to a folder containing " "coordinates files to compare the coordinates there " "contained when --compare_plots is enabled (useful for " "procustes analysis plots). For directories: hidden " "files, sub-directories, 'Icon?' and files suffixed by " "'_procrustes_results.txt' will be ignored.")), make_option('-m', '--map_fp', type="existing_filepath", help='path to a metadata mapping file') ] script_info['optional_options'] = [ make_option('--number_of_axes', type=int,