def get_arguments() -> ModuleArgs:
""" Build and return arguments. """
args = ModuleArgs('Additional analysis', 'asf')
args.add_analysis_toggle('--asf',
dest='asf',
action='store_true',
default=False,
help="Run active site finder analysis.")
return args
def get_arguments() -> ModuleArgs:
""" Build and return arguments. No extra options beyond a switch to enable """
args = ModuleArgs('Additional analysis', 'pfam2go')
args.add_analysis_toggle('--pfam2go',
dest='pfam2go',
action='store_true',
default=False,
help="Run Pfam to Gene Ontology mapping module.")
return args
def get_arguments() -> ModuleArgs:
""" Build and return arguments. No extra options beyond a switch to enable """
args = ModuleArgs('Additional analysis', 'tta')
args.add_analysis_toggle('--tta',
dest='tta',
action='store_true',
default=False,
help="Run TTA codon detection module.")
return args
def get_arguments() -> ModuleArgs:
""" Builds the module args """
args = ModuleArgs('TIGRFam options', 'tigrfam')
args.add_analysis_toggle('tigrfam',
dest='tigrfam',
action='store_true',
default=False,
help="Annotate clusters using TIGRFam profiles.")
return args
def get_arguments() -> ModuleArgs:
""" Build and return arguments. No extra options beyond a switch to enable """
args = ModuleArgs('Additional analysis', 'cassis')
args.add_analysis_toggle(
'--cassis',
dest='cassis',
action='store_true',
default=False,
help="Motif based prediction of SM gene cluster regions.")
return args
def get_arguments() -> ModuleArgs:
""" Sets up arguments for this module.
"""
args = ModuleArgs('ClusterFinder rule-based options', 'cfrules')
args.add_analysis_toggle('cfrules',
dest='cfrules',
action='store_true',
default=False,
help="Find loose rule-based clusters defined by cluster-finder.")
return args
def get_arguments() -> ModuleArgs:
""" Build and return arguments. No extra options beyond a switch to enable """
args = ModuleArgs('Additional analysis', 'tta', enabled_by_default=True)
args.add_option(
'--tta-threshold',
dest='tta_threshold',
type=float,
default=0.65,
help=
"Lowest GC content to annotate TTA codons at (default: %(default)s).")
return args
def get_arguments() -> ModuleArgs:
""" Constructs commandline arguments and options for this module
"""
args = ModuleArgs('Advanced options', 'hmmdetection')
args.add_option('strictness',
dest='strictness',
type=str,
choices=["strict", "relaxed", "loose"],
default="relaxed",
help=("Defines which level of strictness to use for "
"HMM-based cluster detection, (default: %(default)s)."))
return args
def get_arguments() -> ModuleArgs:
""" Construct the arguments.
Classification is enabled by default, but an extra option for generating
trees is also required.
"""
group = ModuleArgs("Basic analysis options", "smcog", basic_help=True)
group.add_analysis_toggle('--smcog-trees',
dest='smcog_trees',
action='store_true',
default=False,
help="Generate phylogenetic trees of sec. "
"met. cluster orthologous groups.")
return group
def get_arguments() -> ModuleArgs:
""" Sets up arguments for this module. Must return a ModuleArgs object.
override_safeties is only set here to allow for the destinations of the
arguments to not include the 'dummy' prefix for the placeholder
arguments.
"""
args = ModuleArgs('Dummy options', '', override_safeties=True)
args.add_option('--dummy-without-fimo',
dest='without_fimo',
action='store_true',
default=False,
help="Dummy only.")
return args
def get_arguments() -> ModuleArgs:
""" Construct args with options for which genefinding method to use (if any)
"""
args = ModuleArgs('Gene finding options (ignored when ORFs are annotated)',
'genefinding',
basic_help=True)
args.add_option(
'tool',
dest='tool',
default='error',
choices=['glimmerhmm', 'prodigal', 'prodigal-m', 'none', 'error'],
type=str,
help="Specify algorithm used for gene finding: GlimmerHMM, "
"Prodigal, Prodigal Metagenomic/Anonymous mode, or none."
" The 'error' option will raise an error if genefinding is attempted."
" The 'none' option will not run genefinding."
" (default: %(default)s).")
args.add_option('gff3',
dest='gff3',
default="",
action=ReadableFullPathAction,
type=str,
metavar="GFF3_FILE",
help="Specify GFF3 file to extract features from.")
return args
def get_arguments() -> ModuleArgs:
""" Builds the arguments for the HMTL output module """
args = ModuleArgs("Output options", "html", enabled_by_default=True)
args.add_option("--html-title",
dest="html_title",
type=str,
default="",
help=("Custom title for the HTML output page "
"(default is input filename)."))
args.add_option("--html-description",
dest="html_description",
type=str,
default="",
help="Custom description to add to the output.")
args.add_option("--html-start-compact",
dest="html_start_compact",
action='store_true',
default=False,
help="Use compact view by default for overview page.")
return args
def get_arguments() -> ModuleArgs:
""" Builds the module args """
args = ModuleArgs('Full HMMer options', 'fullhmmer')
args.add_analysis_toggle('fullhmmer',
dest='fullhmmer',
action='store_true',
default=False,
help="Run a whole-genome HMMer analysis.")
args.add_option('pfamdb-version',
dest='pfamdb_version',
type=str,
default='latest',
help="PFAM database version number (e.g. 27.0) (default: %(default)s).")
return args
def get_arguments() -> ModuleArgs:
""" Builds the arguments for the HMTL output module """
args = ModuleArgs("Output options", "html", enabled_by_default=True)
args.add_option("--html-title",
dest="html_title",
type=str,
default="",
help=("Custom title for the HTML output page "
"(default is input filename)."))
args.add_option("--html-description",
dest="html_description",
type=str,
default="",
help="Custom description to add to the output.")
return args
def get_arguments() -> ModuleArgs:
""" Builds any commandline argument constructs that may be required
Returns:
an empty or populated ModuleArgs instance
"""
args = ModuleArgs('Additional analysis', 'rre')
args.add_analysis_toggle('run',
dest='run',
default=False, # disabled by default
action='store_true',
help="Run RREFinder precision mode on all RiPP gene clusters.")
args.add_option('cutoff',
dest='cutoff',
type=float,
default=25.0,
help="Bitscore cutoff for RRE pHMM detection (default: 25.0).")
args.add_option('min_length',
dest='min_length',
type=int,
default=50,
help='Minimum amino acid length of RRE domains (default: 50).')
return args
def get_arguments() -> ModuleArgs:
""" Constructs commandline arguments and options for this module
"""
args = ModuleArgs("Advanced options", "sideload")
args.add_option(
"sideload",
dest="sideload",
metavar="JSON",
action=MultipleFullPathAction,
default=[],
help=("Sideload annotations from the JSON file in the given paths. "
"Multiple files can be provided, separated by a comma."))
args.add_option(
"sideload-simple",
dest="sideload_simple",
metavar="ACCESSION:START-END",
action=SideloadAction,
default="",
help=("Sideload a single subregion in record ACCESSION from START "
"to END. Positions are expected to be 0-indexed, "
"with START inclusive and END exclusive."))
return args
def get_arguments() -> ModuleArgs:
""" Sets up arguments for this module. Must return a ModuleArgs object.
override_safeties is only set here to allow for the destinations of the
arguments to not include the 'dummy' prefix for the placeholder
arguments.
"""
args = ModuleArgs('ClusterFinder options', 'cf')
args.add_analysis_toggle(
'borders-only',
dest='borders_only',
action='store_true',
default=False,
help="Only annotate borders of existing clusters.")
args.add_analysis_toggle('create-clusters',
dest='create_clusters',
action='store_true',
default=False,
help="Find extra clusters.")
args.add_option(
'min-cds',
dest='min_cds_features',
metavar="INT",
type=int,
default=5,
help="Minimum size of a ClusterFinder cluster, in number of"
" CDS features (default: %(default)s).")
args.add_option(
'mean-threshold',
dest='cf_threshold',
metavar="FLOAT",
type=float,
default=0.6,
help="Minimum mean probability threshold (default: %(default)s).")
args.add_option('min-pfams',
dest='min_pfams',
metavar="INT",
type=int,
default=5,
help="Minimum number of biosynthetic PFam domains in a"
" ClusterFinder cluster (default: %(default)s).")
return args
def get_arguments() -> ModuleArgs:
""" Return the args for the lanthipeptide module """
args = ModuleArgs('Advanced options', 'lanthi', enabled_by_default=True)
return args
def get_arguments() -> ModuleArgs:
""" Builds the args for the clusterblast module """
args = ModuleArgs('ClusterBlast options', 'cb')
args.add_analysis_toggle('general',
dest='general',
action='store_true',
default=False,
help="Compare identified clusters against a "
"database of antiSMASH-predicted clusters.")
args.add_analysis_toggle('subclusters',
dest='subclusters',
action='store_true',
default=False,
help="Compare identified clusters against known "
"subclusters responsible for synthesising "
"precursors.")
args.add_analysis_toggle('knownclusters',
dest='knownclusters',
action='store_true',
default=False,
help="Compare identified clusters against known "
"gene clusters from the MIBiG database.")
args.add_option('nclusters',
dest='nclusters',
metavar="count",
type=int,
default=10,
help="Number of clusters from ClusterBlast to display,"
" cannot be greater than %d. (default: %%(default)s)" %
get_result_limit())
args.add_option(
'min-homology-scale',
dest='min_homology_scale',
metavar="LIMIT",
type=float,
default=0.0,
help=
"A minimum scaling factor for the query BGC in ClusterBlast results."
" Valid range: 0.0 - 1.0. "
" Warning: some homologous genes may no longer be visible!"
" (default: %(default)s)")
return args
def get_arguments() -> ModuleArgs:
""" Builds the arguments for the HMTL output module """
return ModuleArgs("Output options", "html", enabled_by_default=True)
def get_arguments() -> ModuleArgs:
""" Constructs commandline arguments and options for this module
"""
args = ModuleArgs('Advanced options', '', override_safeties=True)
return args
def get_arguments() -> ModuleArgs:
""" Build arguments, no explicit options as enabled by default """
args = ModuleArgs('Advanced options', 'thio', enabled_by_default=True)
return args
def get_arguments() -> ModuleArgs:
""" Constucts T2PKS module arguments
"""
args = ModuleArgs("Advanced options", "t2pks", enabled_by_default=True)
return args
def get_arguments() -> ModuleArgs:
""" Runs by default, but add minimal's --enable option """
args = ModuleArgs('Advanced options', 'lasso', enabled_by_default=True)
return args
def get_arguments() -> ModuleArgs:
""" Constructs commandline arguments and options for this module
"""
return ModuleArgs('Advanced options', 'hmmdetection')
def get_arguments() -> ModuleArgs:
""" Build and return arguments. No extra options beyond a switch to enable """
args = ModuleArgs('Additional analysis',
'genefunctions',
enabled_by_default=True)
return args
def get_arguments():
return ModuleArgs("Output options", "html", enabled_by_default=True)
def get_arguments() -> ModuleArgs:
""" Construct module arguments and for sub-modules """
args = ModuleArgs('NRPS/PKS options', 'np', enabled_by_default=True)
return args