open Core
open Bistro.EDSL
open Bistro.Std
open Bistro_bioinfo.Std
open File_formats
open Defs

type pcoc_out
type diffsel_out

type det_out =
  | Pcoc_out
  | Diffsel_out

type det_result = {
  dataset : Dataset.t ;
  det_meth : det_meth ;
  det_result : det_out directory workflow ;
  }

type dataset_res = {
  model_prefix : string ;
  tree_prefix : string ;
  res_by_tools: det_result list ;
  merged_results : text_file workflow ;
  plot_merged_results : svg workflow
  }

val pcoc :
  ?plot_complete : bool ->
  ?gamma : bool ->
  faa : aminoacid_fasta workflow ->
  tree : _ workflow ->
  (*[`pcoc]*) det_out directory workflow

val pcoc_selector :
    (*[`pcoc]*) det_out directory workflow ->
    text_file workflow

val diffsel :
  phy_n : nucleotide_phylip workflow ->
  tree : _ workflow ->
  w_every : int ->
  n_cycles: int ->
  (*[`diffsel]*) det_out directory workflow

val diffsel_selector :
    (*[`diffsel]*) det_out directory workflow ->
    text_file workflow

val merge_results :
  res_by_tools : det_result list ->
  text_file workflow

val plot_merge_results :
    res_by_tools : det_result list ->
    tree : _ workflow ->
    faa : aminoacid_fasta workflow ->
    tsv : text_file workflow ->
    svg workflow