Copyright	(c) Dominik Schrempf 2018
License	GPL-3.0-or-later
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

SLynx.Simulate.Options

Description

Creation date: Sun Oct 7 17:29:45 2018.

Available options: -h,--help Show this help text -v,--version Show version -t,--tree-file NAME Specify tree file NAME -s,--substitution-model MODEL Set the phylogenetic substitution model; available models are shown below -m,--mixture-model MODEL Set the phylogenetic mixture model; available models are shown below -l,--length NUMBER Set alignment length to NUMBER -e,--edm-file NAME empirical distribution model file NAME in Phylobayes format -w,--mixture-model-weights [DOUBLE,DOUBLE,...] weights of mixture model components -g,--gamma-rate-heterogeneity (NCAT, SHAPE) number of gamma rate categories and shape parameter -e,--seed [INT] Set seed for the random number generator; list of 32 bit integers with up to 256 elements (default: [0]) -q,--quiet Be quiet -o,--output-file NAME Specify output file NAME

Synopsis

Documentation

type GammaRateHeterogeneityParams = (Int, Double) Source #

Number of gamma rate categories and alpha parameter.

data SimulateArguments Source #

Arguments needed to simulate sequences.

Constructors

SimulateArguments
Fields argsTreeFile :: FilePath argsSubstitutionModelString :: Maybe String argsMixtureModelString :: Maybe String argsEDMFile :: Maybe FilePath argsSiteprofilesFiles :: Maybe [FilePath] argsMixtureWeights :: Maybe [Double] argsGammaParams :: Maybe GammaRateHeterogeneityParams argsLength :: Int argsSeed :: Seed

Instances

Eq SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods (==) :: SimulateArguments -> SimulateArguments -> Bool # (/=) :: SimulateArguments -> SimulateArguments -> Bool #
Show SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods showsPrec :: Int -> SimulateArguments -> ShowS # show :: SimulateArguments -> String # showList :: [SimulateArguments] -> ShowS #
Generic SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Associated Types type Rep SimulateArguments :: Type -> Type # Methods from :: SimulateArguments -> Rep SimulateArguments x # to :: Rep SimulateArguments x -> SimulateArguments #
ToJSON SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods toJSON :: SimulateArguments -> Value # toEncoding :: SimulateArguments -> Encoding # toJSONList :: [SimulateArguments] -> Value # toEncodingList :: [SimulateArguments] -> Encoding #
FromJSON SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods parseJSON :: Value -> Parser SimulateArguments # parseJSONList :: Value -> Parser [SimulateArguments] #
Reproducible SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options Methods inFiles :: SimulateArguments -> [FilePath] # outSuffixes :: SimulateArguments -> [String] # getSeed :: SimulateArguments -> Maybe Seed # setSeed :: SimulateArguments -> Vector Word32 -> SimulateArguments # parser :: Parser SimulateArguments # cmdName :: String # cmdDsc :: [String] # cmdFtr :: [String] #
type Rep SimulateArguments Source #
Instance details Defined in SLynx.Simulate.Options type Rep SimulateArguments = D1 (MetaData "SimulateArguments" "SLynx.Simulate.Options" "slynx-0.4.0-J2c9FdWj9XMF4YSARfQCCD" False) (C1 (MetaCons "SimulateArguments" PrefixI True) (((S1 (MetaSel (Just "argsTreeFile") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 FilePath) :: S1 (MetaSel (Just "argsSubstitutionModelString") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe String))) :: (S1 (MetaSel (Just "argsMixtureModelString") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe String)) :: S1 (MetaSel (Just "argsEDMFile") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe FilePath)))) :: ((S1 (MetaSel (Just "argsSiteprofilesFiles") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe [FilePath])) :: S1 (MetaSel (Just "argsMixtureWeights") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe [Double]))) :: (S1 (MetaSel (Just "argsGammaParams") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe GammaRateHeterogeneityParams)) :: (S1 (MetaSel (Just "argsLength") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int) :: S1 (MetaSel (Just "argsSeed") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Seed))))))

simulateArguments :: Parser SimulateArguments Source #

Sub command parser.

simulateFooter :: [String] Source #

The model specification is somewhat complicated, so we need to provide additional help.