INNER CODE UNIT · Python
add_condense_arguments
wwood/singlem · singlem/main.py:255
def add_condense_arguments(parser):
input_condense_arguments = parser.add_argument_group("Input arguments (1+ required)")
input_condense_arguments.add_argument('--input-archive-otu-tables', '--input-archive-otu-table', nargs='+', help="Condense from these archive tables")
input_condense_arguments.add_argument('--input-archive-otu-table-list',
help="Condense from the archive tables newline separated in this file")
input_condense_arguments.add_argument('--input-gzip-archive-otu-table-list',
help="Condense from the gzip'd archive tables newline separated in this file")
output_condense_arguments = parser.add_argument_group("Output arguments (1+ required)")
output_condense_arguments.add_argument('-p', '--taxonomic-profile', metavar='filename', help="output OTU table")
output_condense_arguments.add_argument('--taxonomic-profile-krona', metavar='filename', help='name of krona file to generate.')
output_condense_arguments.add_argument('--output-after-em-otu-table', metavar='filename', help="output OTU table after expectation maximisation has been applied. Note that this table usually contains multiple rows with the same window sequence.")
optional_condense_arguments = parser.add_argument_group("Other options")
optional_condense_arguments.add_argument('--metapackage', help='Set of SingleM packages to use [default: use the default set]')
current_default = CONDENSE_DEFAULT_MIN_TAXON_COVERAGE
optional_condense_arguments.add_argument('--min-taxon-coverage',metavar='FRACTION',
help='Set taxons with less coverage to coverage=0. [default: {}]'.format(current_default), default=current_default, type=float)