{-# LANGUAGE DeriveGeneric #-}
module TLynx.Examine.Options
( ExamineArguments (..),
examineArguments,
)
where
import ELynx.Tools
import Options.Applicative
import TLynx.Parsers
data ExamineArguments = ExamineArguments
{ argsInFile :: FilePath,
argsNewickFormat :: NewickFormat
}
deriving (Eq, Show, Generic)
instance Reproducible ExamineArguments where
inFiles = pure . argsInFile
outSuffixes _ = [".out"]
getSeed _ = Nothing
setSeed = const
parser = examineArguments
cmdName = "examine"
cmdDsc = ["Compute summary statistics of phylogenetic trees."]
instance FromJSON ExamineArguments
instance ToJSON ExamineArguments
examineArguments :: Parser ExamineArguments
examineArguments = ExamineArguments <$> inFile <*> newickFormat
inFile :: Parser FilePath
inFile =
strArgument $ metavar "INPUT-FILE" <> help "Read trees from INPUT-FILE"