Options.hs

{-# LANGUAGE DeriveGeneric #-}

-- |
-- Module      :  TLynx.Shuffle.Options
-- Description :  Options for the connect subcommand
-- Copyright   :  2021 Dominik Schrempf
-- License     :  GPL-3.0-or-later
--
-- Maintainer  :  dominik.schrempf@gmail.com
-- Stability   :  unstable
-- Portability :  portable
--
-- Creation date: Thu Sep 19 15:02:21 2019.
module TLynx.Shuffle.Options
  ( ShuffleArguments (..),
    shuffleArguments,
  )
where

import Data.Aeson
import ELynx.Tools.Options
import ELynx.Tools.Reproduction
import GHC.Generics
import Options.Applicative
import TLynx.Parsers

-- | Arguments of shuffle command.
data ShuffleArguments = ShuffleArguments
  { nwFormat :: NewickFormat,
    nReplicates :: Int,
    inFile :: FilePath,
    argsSeed :: SeedOpt
  }
  deriving (Eq, Show, Generic)

instance Reproducible ShuffleArguments where
  inFiles = pure . inFile
  outSuffixes _ = [".tree"]
  getSeed = Just . argsSeed
  setSeed a s = a {argsSeed = s}
  parser = shuffleArguments
  cmdName = "shuffle"
  cmdDsc =
    [ "Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and leaves)."
    ]

instance FromJSON ShuffleArguments

instance ToJSON ShuffleArguments

-- | Parse arguments of shuffle command.
shuffleArguments :: Parser ShuffleArguments
shuffleArguments = ShuffleArguments <$> newickFormat <*> n <*> file <*> seedOpt

n :: Parser Int
n =
  option auto $
    long "replicates"
      <> short 'n'
      <> metavar "N"
      <> value 1
      <> help
        "Number of trees to generate"

file :: Parser FilePath
file =
  strArgument $ metavar "TREE-FILE" <> help "File containing a Newick tree"