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