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', '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: """ 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: """ 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: """ 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: """ 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: """ 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: """ 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: """ 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( 'diamond-executable', dest='diamond_executable', metavar='filename', type=str, default='diamond', help="The path to the diamond executable. (default: %(default)s)") 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