update wrt world

lib/alistats.ml

 open Core
 open Phylogenetics
+open Bistro
 
 let ok_exn err = function
   | Ok x -> x
@@ -8,7 +9,7 @@ let ok_exn err = function
 let is_gc ?pos i c =
   match pos with
   | Some p when not ((i mod 3) = p) -> false
-  | _ -> c = 'g' || c = 'G' || c = 'c' || c = 'C'
+  | _ -> Char.(c = 'g' || c = 'G' || c = 'c' || c = 'C')
 
 let strings_from_fasta fa =
   match Alignment.from_fasta fa with
@@ -29,7 +30,7 @@ let seq_gc ?pos seqs =
     )
   in
   let gc_counts = Array.map seqs ~f:(fun seq ->
-      let len = if pos <> None then String.length seq / 3 else String.length seq in
+      let len = if Option.is_some pos then String.length seq / 3 else String.length seq in
       let sum = String.foldi ~init:0 ~f:(fun i a c -> a + if is_gc ?pos i c then 1 else 0) seq in
       float len, float sum
     )
@@ -76,7 +77,7 @@ let command =
       main ~alignment
     ]
 
-let%pworkflow histogram (fa : #Bistro.fasta Bistro.pworkflow) =
+let%pworkflow histogram (fa : #fasta file) =
   let al = ok_exn Alignment.show_parsing_error @@ Alignment.from_fasta [%path fa] in
   let float_array_of_int_list x =
     Array.of_list x

lib/bppsuite.ml

@@ -142,10 +142,10 @@ rate_distribution=Constant()
       )
     ]
 
-  let alignment run_bppseqgen_multi_profiles : nucleotide_fasta pworkflow =
+  let alignment run_bppseqgen_multi_profiles : nucleotide_fasta file =
     Workflow.select run_bppseqgen_multi_profiles ["seq.fa"]
 
-  let info run_bppseqgen_multi_profiles : text_file pworkflow =
+  let info run_bppseqgen_multi_profiles : text file =
     Workflow.select run_bppseqgen_multi_profiles ["seq.fa.info"]
 
 end
@@ -166,7 +166,7 @@ let conf_file_bppseqman_fna2faa ~fna =
            |}
   ]
 
-let fna2faa (fna : nucleotide_fasta pworkflow) : aminoacid_fasta pworkflow =
+let fna2faa (fna : nucleotide_fasta file) : aminoacid_fasta file =
   Workflow.shell ~descr:"bppsuite.fna2faa" [
     cmd "bppseqman" ~img [
       assign "param" (file_dump (conf_file_bppseqman_fna2faa ~fna)) ;
@@ -197,14 +197,14 @@ let conf_file_bppseqman_faa2phy ~faa =
            |}
   ]
 
-let fna2phy ~(fna: nucleotide_fasta pworkflow) : nucleotide_phylip pworkflow =
+let fna2phy ~(fna: nucleotide_fasta file) : nucleotide_phylip file =
   Workflow.shell ~descr:"bppsuite.fna2phy_interleaved" [
     cmd "bppseqman" ~img [
       assign "param" (file_dump (conf_file_bppseqman_fna2phy ~fna)) ;
     ]
   ]
 
-let faa2phy ~(faa: aminoacid_fasta pworkflow) : aminoacid_phylip pworkflow =
+let faa2phy ~(faa: aminoacid_fasta file) : aminoacid_phylip file =
   Workflow.shell ~descr:"bppsuite.faa2phy_interleaved" [
     cmd "bppseqman" ~img [
       assign "param" (file_dump (conf_file_bppseqman_faa2phy ~faa)) ;
@@ -212,7 +212,7 @@ let faa2phy ~(faa: aminoacid_fasta pworkflow) : aminoacid_phylip pworkflow =
   ]
 
 
-let paste_fna  ~(fna_l: nucleotide_fasta pworkflow list) : nucleotide_fasta pworkflow =
+let paste_fna  ~(fna_l: nucleotide_fasta file list) : nucleotide_fasta file =
   Workflow.shell ~descr:"bppsuite.catfasta" [
     cmd "catfasta2phyml.pl" ~stdout:dest ~img (List.concat [
         [string "-f" ] ;

lib/bppsuite.mli

@@ -4,34 +4,34 @@ open File_formats
 module Bppseqgen : sig
   val multi_profiles :
     ?descr : string ->
-    profile_f: text_file pworkflow ->
-    profile_c: text_file pworkflow ->
-    input_tree: nhx pworkflow ->
+    profile_f: text file ->
+    profile_c: text file ->
+    input_tree: nhx file ->
     hypothesis:Convergence_hypothesis.t ->
     seed:int ->
-    [`bppseqgen] dworkflow
+    [`bppseqgen] directory
 
   val alignment :
-    [`bppseqgen] dworkflow ->
-    nucleotide_fasta pworkflow
+    [`bppseqgen] directory ->
+    nucleotide_fasta file
 
   val info :
-    [`bppseqgen] dworkflow ->
-    text_file pworkflow
+    [`bppseqgen] directory ->
+    text file
 end
 
 val fna2faa :
-  nucleotide_fasta pworkflow ->
-  aminoacid_fasta pworkflow
+  nucleotide_fasta file ->
+  aminoacid_fasta file
 
 val fna2phy :
-  fna: nucleotide_fasta pworkflow ->
-  nucleotide_phylip pworkflow
+  fna: nucleotide_fasta file ->
+  nucleotide_phylip file
 
 val faa2phy :
-  faa: aminoacid_fasta pworkflow ->
-  aminoacid_phylip pworkflow
+  faa: aminoacid_fasta file ->
+  aminoacid_phylip file
 
 val paste_fna:
-  fna_l: nucleotide_fasta pworkflow list ->
-  nucleotide_fasta pworkflow
+  fna_l: nucleotide_fasta file list ->
+  nucleotide_fasta file

lib/convergence_detection.ml

@@ -3,17 +3,17 @@ open Bistro.Shell_dsl
 open Bistro
 
 type result = [
-  | `Pcoc of [`pcoc] dworkflow
-  | `Pcoc_gamma of [`pcoc] dworkflow
-  | `Pcoc_C60 of [`pcoc] dworkflow
-  | `Diffsel of [`diffsel] dworkflow
-  | `Identical_LG of [`identical] dworkflow
-  | `Identical_WAG of [`identical] dworkflow
-  | `Topological_LG of [`topological] dworkflow
-  | `Topological_WAG of [`topological] dworkflow
-  | `Tdg09 of [`tdg09] dworkflow
-  | `Multinomial of text_file pworkflow
-  | `Msd of [`msd] dworkflow * float
+  | `Pcoc of [`pcoc] directory
+  | `Pcoc_gamma of [`pcoc] directory
+  | `Pcoc_C60 of [`pcoc] directory
+  | `Diffsel of [`diffsel] directory
+  | `Identical_LG of [`identical] directory
+  | `Identical_WAG of [`identical] directory
+  | `Topological_LG of [`topological] directory
+  | `Topological_WAG of [`topological] directory
+  | `Tdg09 of [`tdg09] directory
+  | `Multinomial of text file
+  | `Msd of [`msd] directory * float
 ]
 
 let meth_string_of_result = function
@@ -34,11 +34,11 @@ type dataset_res = {
   tree_prefix : string ;
   dataset : Dataset.t ;
   res_by_tools: result list ;
-  merged_results : text_file pworkflow ;
-  plot_merged_results : svg pworkflow ;
+  merged_results : text file ;
+  plot_merged_results : svg file ;
 }
 
-let merge_results ?fna_infos ~(res_by_tools : result list) () : text_file pworkflow =
+let merge_results ?fna_infos ~(res_by_tools : result list) () : text file =
   let command = List.map res_by_tools ~f:(fun res ->
       let w = match res with
         | `Pcoc d -> Pcoc.results d
@@ -78,7 +78,7 @@ let merge_results ?fna_infos ~(res_by_tools : result list) () : text_file pworkf
     ] ;
   ]
 
-let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?identical ?topological ?pcoc ?pcoc_v2 ?pcoc_pcp ?diffsel ?diffseldsparse () : text_file pworkflow =
+let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?identical ?topological ?pcoc ?pcoc_v2 ?pcoc_pcp ?diffsel ?diffseldsparse () : text file =
   Workflow.shell ~descr:"convergence_detection.merge_results" [
     cmd "python" ~img:Env.env_py [
       file_dump (string Scripts.merge_det_results) ;
@@ -97,7 +97,7 @@ let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?identical ?topol
     ] ;
   ]
 
-let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~tree ~faa ~tsv (): svg pworkflow =
+let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~tree ~faa ~tsv (): svg file =
   let img = Env.env_pcoc in
   (* use of pcoc env due to its working X server for dra plot with ete3 *)
   let meths = List.map res_by_tools ~f:(fun res ->

lib/convergence_detection.mli

@@ -2,17 +2,17 @@ open Bistro
 open File_formats
 
 type result = [
-  | `Pcoc of [`pcoc] dworkflow
-  | `Pcoc_gamma of [`pcoc] dworkflow
-  | `Pcoc_C60 of [`pcoc] dworkflow
-  | `Diffsel of [`diffsel] dworkflow
-  | `Identical_LG of [`identical] dworkflow
-  | `Identical_WAG of [`identical] dworkflow
-  | `Topological_LG of [`topological] dworkflow
-  | `Topological_WAG of [`topological] dworkflow
-  | `Tdg09 of [`tdg09] dworkflow
-  | `Multinomial of text_file pworkflow
-  | `Msd of [`msd] dworkflow * float
+  | `Pcoc of [`pcoc] directory
+  | `Pcoc_gamma of [`pcoc] directory
+  | `Pcoc_C60 of [`pcoc] directory
+  | `Diffsel of [`diffsel] directory
+  | `Identical_LG of [`identical] directory
+  | `Identical_WAG of [`identical] directory
+  | `Topological_LG of [`topological] directory
+  | `Topological_WAG of [`topological] directory
+  | `Tdg09 of [`tdg09] directory
+  | `Multinomial of text file
+  | `Msd of [`msd] directory * float
 ]
 
 val meth_string_of_result : result -> string
@@ -22,58 +22,58 @@ type dataset_res = {
   tree_prefix : string ;
   dataset : Dataset.t ;
   res_by_tools: result list ;
-  merged_results : text_file pworkflow ;
-  plot_merged_results : svg pworkflow
+  merged_results : text file ;
+  plot_merged_results : svg file
 }
 
 val merge_results :
-  ?fna_infos:text_file pworkflow ->
+  ?fna_infos:text file ->
   res_by_tools : result list ->
   unit ->
-  text_file pworkflow
+  text file
 
 val merge_result_tables :
-  ?fna_infos:text_file pworkflow ->
-  ?oracle:text_file pworkflow ->
-  ?multinomial:text_file pworkflow ->
-  ?tdg09:text_file pworkflow ->
-  ?identical:text_file pworkflow ->
-  ?topological:text_file pworkflow ->
-  ?pcoc:text_file pworkflow ->
-  ?pcoc_v2:text_file pworkflow ->
-  ?pcoc_pcp:text_file pworkflow ->
-  ?diffsel:text_file pworkflow ->
-  ?diffseldsparse:text_file pworkflow ->
+  ?fna_infos:text file ->
+  ?oracle:text file ->
+  ?multinomial:text file ->
+  ?tdg09:text file ->
+  ?identical:text file ->
+  ?topological:text file ->
+  ?pcoc:text file ->
+  ?pcoc_v2:text file ->
+  ?pcoc_pcp:text file ->
+  ?diffsel:text file ->
+  ?diffseldsparse:text file ->
   unit ->
-  text_file pworkflow
+  text file
 
 val plot_merge_results :
-  ? t_choices : text_file pworkflow ->
+  ? t_choices : text file ->
   plot_all_sites: bool ->
   res_by_tools : result list ->
-  tree:nhx pworkflow ->
-  faa:aminoacid_fasta pworkflow ->
-  tsv:text_file pworkflow ->
+  tree:nhx file ->
+  faa:aminoacid_fasta file ->
+  tsv:text file ->
   unit ->
-  svg pworkflow
+  svg file
 
 val plot_convergent_sites :
   ?plot_all_sites:bool ->
-  alignment:aminoacid_fasta pworkflow ->
-  detection_results:text_file pworkflow ->
-  tree:nhx pworkflow ->
+  alignment:aminoacid_fasta file ->
+  detection_results:text file ->
+  tree:nhx file ->
   unit ->
-  svg pworkflow
+  svg file
 
 val recall_precision_curve :
-  text_file pworkflow ->
-  svg pworkflow
+  text file ->
+  svg file
 
 val oracle :
   n_h0:int ->
   n_ha:int ->
-  text_file pworkflow
+  text file
 
 val recall_precision_auc_table :
-  text_file pworkflow ->
+  text file ->
   (string * float) array workflow

lib/convergence_hypothesis.ml

@@ -14,7 +14,7 @@ type t = model
 let string_of_float_without_dot f = (* to avoid things like "H0_NeG4._NeC2." *)
   let int_value = int_of_float f in
   let rounded = int_value |> float_of_int in
-  if rounded -. f = 0. then string_of_int int_value else string_of_float f
+  if Float.(rounded -. f = 0.) then string_of_int int_value else string_of_float f
 let string_of_nes nes = match nes with
   | Fixed g -> "NeG" ^ (string_of_float_without_dot g)
   | Variable (g, c) -> "NeG" ^ (string_of_float_without_dot g) ^ "_NeC_" ^ (string_of_float_without_dot c)

lib/debug.ml

@@ -24,26 +24,19 @@ let eval w =
 let path w =
   with_workflow (Workflow.eval_path w) ~f:(fun x -> x)
 
-let less w =
-  Sys.command (sprintf "less %s" (path w))
-  |> ignore
+let command fmt =
+  Printf.ksprintf (fun s -> ignore (Sys.command s : int)) fmt
 
-let firefox w =
-  Sys.command (sprintf "firefox %s" (path w))
-  |> ignore
+let less w = command "less %s" (path w)
 
-let seaview w =
-  Sys.command (sprintf "seaview %s" (path w))
-  |> ignore
+let firefox w = command "firefox %s" (path w)
 
-let evince w =
-  Sys.command (sprintf "evince %s" (path w))
-  |> ignore
+let seaview w = command "seaview %s" (path w)
+
+let evince w = command "evince %s" (path w)
 
 let workflow_of_template t =
   let open Bistro.Shell_dsl in
   Workflow.shell [
     cmd "cp" [ file_dump t ; dest ]
   ]
-
-

lib/detection_pipeline.ml

@@ -3,9 +3,9 @@ open File_formats
 
 module type Dataset = sig
   type t
-  val tree : t -> nhx pworkflow
+  val tree : t -> nhx file
 
-  val nucleotide_alignment : t -> nucleotide_fasta pworkflow
+  val nucleotide_alignment : t -> nucleotide_fasta file
 end
 
 module Make(D : Dataset) = struct

lib/diffsel.ml

@@ -50,7 +50,7 @@ echo end_it=$end_it
 |}
 
 
-let diffsel ~(phy_n:nucleotide_phylip pworkflow) ~(tree: _ pworkflow) ~(w_every:int) ~(n_cycles: int) ?(descr = "") ?seed () : [`diffsel] dworkflow =
+let diffsel ~(phy_n:nucleotide_phylip file) ~(tree: _ file) ~(w_every:int) ~(n_cycles: int) ?(descr = "") ?seed () : [`diffsel] directory =
   let env = Env.env_diffsel in
   let tmp_tree = tmp // "myrun.tree" in
   let tmp_ali = tmp // "myrun.ali" in
@@ -84,7 +84,7 @@ let diffsel ~(phy_n:nucleotide_phylip pworkflow) ~(tree: _ pworkflow) ~(w_every:
     )
   ]
 
-let check_conv run_diffsel : directory pworkflow =
+let check_conv run_diffsel : [`diffsel_check_conv] directory =
   let env = Env.env_r in
   let script = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in
   let trace = Workflow.select run_diffsel ["myrun.trace"] in
@@ -110,7 +110,7 @@ let check_conv run_diffsel : directory pworkflow =
     )
   ]
 
-let selector run_diffsel : text_file pworkflow =
+let selector run_diffsel : text file =
   let env = Env.env_diffsel in
   let package = tmp // "diffsel_script_utils.py" in
   let script = tmp // "diffsel_analyze_result.py" in

lib/diffsel.mli

@@ -2,19 +2,19 @@ open Bistro
 open File_formats
 
 val diffsel :
-  phy_n:nucleotide_phylip pworkflow ->
-  tree:_ pworkflow ->
+  phy_n:nucleotide_phylip file ->
+  tree:_ file ->
   w_every:int ->
   n_cycles:int ->
   ?descr:string ->
   ?seed:int ->
   unit ->
-  [`diffsel] dworkflow
+  [`diffsel] directory
 
 val selector :
-  [`diffsel] dworkflow ->
-  text_file pworkflow
+  [`diffsel] directory ->
+  text file
 
 val check_conv :
-  [`diffsel] dworkflow ->
-  directory pworkflow
+  [`diffsel] directory ->
+  [`diffsel_check_conv] directory

lib/diffseldsparse.ml

@@ -43,8 +43,8 @@ echo end_it=$end_it
 
 let diffseldsparse
     ?pi ?shiftprob ?eps
-    ~(alignment:nucleotide_phylip pworkflow) ~(tree: _ pworkflow)
-    ~(w_every:int) ~(n_cycles: int) () : [`diffseldsparse] dworkflow =
+    ~(alignment:nucleotide_phylip file) ~(tree: _ file)
+    ~(w_every:int) ~(n_cycles: int) () : [`diffseldsparse] directory =
   let tmp_tree = tmp // "myrun.tree" in
   let tmp_ali = tmp // "myrun.ali" in
   let dest_tree = dest // "myrun.tree" in
@@ -79,7 +79,7 @@ let diffseldsparse
     )
   ]
 
-let check_conv run_diffseldsparse : directory pworkflow =
+let check_conv run_diffseldsparse : [`diffseldsparse_check_conv] directory =
   let script = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in
   let trace = Workflow.select run_diffseldsparse ["myrun.trace"] in
   let out = dest // "out.html" in
@@ -123,7 +123,7 @@ let readdiffseldsparse run =
     )
   ]
 
-let posterior_probabilities run_diffseldsparse : text_file pworkflow =
+let posterior_probabilities run_diffseldsparse : text file =
   let tmp_tree = tmp // "myrun.tree" in
   let tmp_ali = tmp // "myrun.ali" in
   let dep_tree = (dep run_diffseldsparse) // "myrun.tree" in

lib/diffseldsparse.mli

@@ -5,25 +5,25 @@ val diffseldsparse :
   ?pi:float ->
   ?shiftprob:float * float ->
   ?eps:float ->
-  alignment:nucleotide_phylip pworkflow ->
-  tree:_ pworkflow ->
+  alignment:nucleotide_phylip file ->
+  tree:_ file ->
   w_every:int ->
   n_cycles:int ->
   unit ->
-  [`diffseldsparse] dworkflow
+  [`diffseldsparse] directory
 
 val posterior_probabilities :
-  [`diffseldsparse] dworkflow ->
-  text_file pworkflow
+  [`diffseldsparse] directory ->
+  text file
 
 val readdiffseldsparse :
-  [`diffseldsparse] dworkflow ->
-  [`readdiffseldsparse] dworkflow
+  [`diffseldsparse] directory ->
+  [`readdiffseldsparse] directory
 
 val check_conv :
-  [`diffseldsparse] dworkflow ->
-  directory pworkflow
+  [`diffseldsparse] directory ->
+  [`diffseldsparse_check_conv] directory
 
 val results :
-  [`readdiffseldsparse] dworkflow ->
-  text_file pworkflow
+  [`readdiffseldsparse] directory ->
+  text file

lib/dune

 (library
  (name reviewphiltrans)
- (libraries bistro.bioinfo bistro.utils gzt ocaml-r.graphics ocaml-r.grDevices phylogenetics.convergence reviewphiltrans_toolbox )
+ (libraries biotk biotope bistro.utils ocaml-r.graphics ocaml-r.grDevices phylogenetics.convergence reviewphiltrans_toolbox)
  (preprocess
   (pps ppx_jane ppx_csv_conv bistro.ppx ppx_here)))
 

lib/file_formats.ml

 open Bistro
 
 class type nhx = object
-  inherit text_file
+  inherit text
   method format : [`nhx]
 end
 
 class type nw = object
-  inherit text_file
+  inherit text
   method format : [`nw]
 end
 
 class type diffsel_tree = object
-  inherit text_file
+  inherit text
   method format : [`diffsel_tree]
 end
 
 class type topological_tree = object
-  inherit text_file
+  inherit text
   method format : [`topological_tree]
 end
 
@@ -31,10 +31,10 @@ class type aminoacid_fasta = object
 end
 
 class type nucleotide_phylip = object
-  inherit text_file
+  inherit text
   method format : [`Nucleotide]
 end
 class type aminoacid_phylip = object
-  inherit text_file
+  inherit text
   method format : [`Aminoacid]
 end

lib/identical.ml

@@ -91,7 +91,7 @@ let bppancestor ?(descr="") ~faa ~tree ~config : _ workflow =
     )
   ]
 
-let identical ?(descr="") ~(tree_id:_ pworkflow) ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) ~prot_model () : [`identical] dworkflow =
+let identical ?(descr="") ~(tree_id:_ file) ~(tree_sc:_ file) ~(faa:aminoacid_fasta file) ~prot_model () : [`identical] directory =
   let config = [assign "model" (string prot_model)] in
   let out1 = dest // "out1.tsv" in
   let out2 = dest // "out2.tsv" in
@@ -109,5 +109,5 @@ let identical ?(descr="") ~(tree_id:_ pworkflow) ~(tree_sc:_ pworkflow) ~(faa:am
     ]
   ]
 
-let results run_identical : text_file pworkflow =
+let results run_identical : text file =
   Workflow.select run_identical ["out1.tsv"]

lib/msd.ml

@@ -5,7 +5,7 @@ open File_formats
 
 let img = Env.env_msd
 
-let msd ?(descr="") ~e ~(faa : aminoacid_fasta pworkflow) ~(tree_sc : _ pworkflow) : [`msd] dworkflow =
+let msd ?(descr="") ~e ~(faa : aminoacid_fasta file) ~(tree_sc : _ file) : [`msd] directory =
   let map_table = dest // "map.tsv" in
   let tree_nw = dest // "tree.nw" in
   let out = dest // "out.tsv" in
@@ -42,7 +42,7 @@ let msd ?(descr="") ~e ~(faa : aminoacid_fasta pworkflow) ~(tree_sc : _ pworkflo
     ];
   ]
 
-let results run_msd : text_file pworkflow =
+let results run_msd : text file =
   Workflow.shell ~descr:"convergence_detection.parse_msd" [
     cmd "python" ~img [
       file_dump (string Scripts.parse_output_msd) ;

lib/multinomial.ml

@@ -3,7 +3,7 @@ open Bistro
 open Bistro.Shell_dsl
 open File_formats
 
-let multinomial ?(descr="") ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) : text_file pworkflow =
+let multinomial ?(descr="") ~(tree_sc:_ file) ~(faa:aminoacid_fasta file) : text file =
   let img = Env.env_py in
   Workflow.shell ~descr:("calc_multinomial."^descr) [
     mkdir_p dest;
@@ -15,7 +15,7 @@ let multinomial ?(descr="") ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkfl
     ]
   ]
 
-let%pworkflow multinomial_ocaml_implementation ~meth ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) (* : text_file pworkflow *) =
+let%pworkflow multinomial_ocaml_implementation ~meth ~(tree_sc:_ file) ~(faa:aminoacid_fasta file) (* : text file *) =
   let open Phylogenetics in
   let open Phylogenetics_convergence in
   let module MT = Multinomial_test in

lib/pcoc.ml

@@ -5,7 +5,7 @@ open File_formats
 
 let img = Env.env_pcoc
 
-let pcoc ?(descr = "") ?plot_complete ?gamma ?catx_est ?max_gap_per_pos ?max_gap_per_conv_leaf ~(faa:aminoacid_fasta pworkflow) ~(tree:_ workflow) (): [`pcoc] dworkflow =
+let pcoc ?(descr = "") ?plot_complete ?gamma ?catx_est ?max_gap_per_pos ?max_gap_per_conv_leaf ~(faa:aminoacid_fasta file) ~(tree:_ workflow) (): [`pcoc] directory =
   Workflow.shell ~descr:("convergence_detection.pcoc."^descr) [
     cmd "pcoc_det.py" ~img [
       opt "-t" dep tree;
@@ -20,7 +20,7 @@ let pcoc ?(descr = "") ?plot_complete ?gamma ?catx_est ?max_gap_per_pos ?max_gap
     ]
   ]
 
-let results run_pcoc : text_file pworkflow =
+let results run_pcoc : text file =