| Copyright | 2021 Dominik Schrempf |
|---|---|
| License | GPL-3.0-or-later |
| Maintainer | [email protected] |
| 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
- type GammaRateHeterogeneityParams = (Int, Double)
- data MixtureModelGlobalNormalization
- data SimulateArguments = SimulateArguments {
- argsTreeFile :: FilePath
- argsSubstitutionModelString :: Maybe String
- argsMixtureModelString :: Maybe String
- argsMixtureModelGlobalNormalization :: MixtureModelGlobalNormalization
- argsEDMFile :: Maybe FilePath
- argsSiteprofilesFiles :: Maybe [FilePath]
- argsMixtureWeights :: Maybe [Double]
- argsGammaParams :: Maybe GammaRateHeterogeneityParams
- argsLength :: Int
- argsSeed :: SeedOpt
- simulateArguments :: Parser SimulateArguments
- simulateFooter :: [String]
Documentation
type GammaRateHeterogeneityParams = (Int, Double) Source #
Number of gamma rate categories and alpha parameter.
data MixtureModelGlobalNormalization Source #
Constructors
| GlobalNormalization | |
| LocalNormalization |
Instances
data SimulateArguments Source #
Arguments needed to simulate sequences.
Constructors
| SimulateArguments | |
Fields
| |
Instances
| FromJSON SimulateArguments Source # | |||||
Defined in SLynx.Simulate.Options Methods parseJSON :: Value -> Parser SimulateArguments # parseJSONList :: Value -> Parser [SimulateArguments] # | |||||
| ToJSON SimulateArguments Source # | |||||
Defined in SLynx.Simulate.Options Methods toJSON :: SimulateArguments -> Value # toEncoding :: SimulateArguments -> Encoding # toJSONList :: [SimulateArguments] -> Value # toEncodingList :: [SimulateArguments] -> Encoding # omitField :: SimulateArguments -> Bool # | |||||
| Reproducible SimulateArguments Source # | |||||
Defined in SLynx.Simulate.Options Methods inFiles :: SimulateArguments -> [FilePath] # outSuffixes :: SimulateArguments -> [String] # getSeed :: SimulateArguments -> Maybe SeedOpt # setSeed :: SimulateArguments -> SeedOpt -> SimulateArguments # | |||||
| Generic SimulateArguments Source # | |||||
Defined in SLynx.Simulate.Options Associated Types
Methods from :: SimulateArguments -> Rep SimulateArguments x # to :: Rep SimulateArguments x -> SimulateArguments # | |||||
| Show SimulateArguments Source # | |||||
Defined in SLynx.Simulate.Options Methods showsPrec :: Int -> SimulateArguments -> ShowS # show :: SimulateArguments -> String # showList :: [SimulateArguments] -> ShowS # | |||||
| Eq SimulateArguments Source # | |||||
Defined in SLynx.Simulate.Options Methods (==) :: SimulateArguments -> SimulateArguments -> Bool # (/=) :: SimulateArguments -> SimulateArguments -> Bool # | |||||
| type Rep SimulateArguments Source # | |||||
Defined in SLynx.Simulate.Options type Rep SimulateArguments = D1 ('MetaData "SimulateArguments" "SLynx.Simulate.Options" "slynx-0.8.0.0-H6mDyksKj74L7hX3CQSr0A" '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 "argsMixtureModelGlobalNormalization") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 MixtureModelGlobalNormalization) :*: 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 SeedOpt)))))) | |||||
simulateArguments :: Parser SimulateArguments Source #
Sub command parser.
simulateFooter :: [String] Source #
The model specification is somewhat complicated, so we need to provide additional help.