INNER CODE UNIT · Python
add_less_common_pipe_arguments
wwood/singlem · singlem/main.py:133
def add_less_common_pipe_arguments(argument_group, extra_args=False):
argument_group.add_argument('--archive-otu-table', metavar='filename', help='output OTU table in archive format for making DBs etc. [default: unused]')
argument_group.add_argument('--metapackage', help='Set of SingleM packages to use [default: use the default set]')
argument_group.add_argument('--read-chunk-size',
type=int,
metavar='num_reads',
help='Number of reads per chunk. Requires unwrapped sequence input. Both FASTA and FASTQ inputs are supported; the chunk size is the number of reads in each chunk. Requires --read-chunk-number.')
argument_group.add_argument('--read-chunk-number',
type=int,
metavar='chunk_number',
help='Process only this specific chunk number (1-based index). Requires --read-chunk-size.')
argument_group.add_argument('--output-jplace', metavar='filename', help='Output a jplace format file for each singlem package to a file starting with this string, each with one entry per OTU. Requires \'%s\' as the --assignment_method [default: unused]' % pipe.PPLACER_ASSIGNMENT_METHOD)
argument_group.add_argument('--singlem-packages', nargs='+', help='SingleM packages to use [default: use the set from the default metapackage]')
argument_group.add_argument('--assignment-singlem-db', '--assignment_singlem_db', help='Use this SingleM DB when assigning taxonomy [default: not set, use the default]')
argument_group.add_argument('--diamond-taxonomy-assignment-performance-parameters',
help='Performance-type arguments to use when calling \'diamond blastx\' during the taxonomy assignment step. [default: use setting defined in metapackage when set, otherwise use \'%s\']' % SearchPipe.DEFAULT_DIAMOND_ASSIGN_TAXONOMY_PERFORMANCE_PARAMETERS,
default=None)
argument_group.add_argument('--evalue',