"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,
