Commit 89c18c48 authored by Carine Rey's avatar Carine Rey
Browse files

specify to pcoc to use c10

parent 57ef1938
......@@ -4,7 +4,7 @@ open Bistro.EDSL
open Bistro_bioinfo.Std
open File_formats
let pcoc ?plot_complete ?gamma ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`pcoc] directory workflow =
let pcoc ?plot_complete ?gamma ?catx_est ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`pcoc] directory workflow =
let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"07022018" () in
workflow ~descr:"convergence_detection.pcoc" [
cmd "pcoc_det.py" ~env [
......@@ -13,6 +13,7 @@ let pcoc ?plot_complete ?gamma ~(faa:aminoacid_fasta workflow) ~(tree:_ workflo
opt "-aa" dep faa ;
opt "-o" ident dest ;
option ( flag string "--gamma" ) gamma;
option ( opt "-CATX_est" int) catx_est;
option ( flag string "--plot --plot_complete_ali" ) plot_complete;
]
]
......
......@@ -4,6 +4,7 @@ open File_formats
val pcoc :
?plot_complete : bool ->
?gamma : bool ->
?catx_est : int ->
faa : aminoacid_fasta workflow ->
tree : _ workflow ->
[`pcoc] directory workflow
......
......@@ -170,8 +170,8 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
let w_every = if preview then 1 else 1 in
let n_cycles = if preview then 10 else 2000 in
match det_meth with
| `Pcoc -> `Pcoc (Pcoc.pcoc ~plot_complete:true ~gamma:false ~faa ~tree:tree_sc)
| `Pcoc_gamma -> `Pcoc_gamma (Pcoc.pcoc ~plot_complete: true ~gamma:true ~faa ~tree:tree_sc)
| `Pcoc -> `Pcoc (Pcoc.pcoc ~catx_est:10 ~plot_complete:true ~gamma:false ~faa ~tree:tree_sc)
| `Pcoc_gamma -> `Pcoc_gamma (Pcoc.pcoc ~catx_est:10 ~plot_complete: true ~gamma:true ~faa ~tree:tree_sc)
| `Tdg09 -> `Tdg09 (Tamuri.tdg09 ~faa ~tree:tree_sc)
| `Diffsel -> `Diffsel (Diffsel.diffsel ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~id:1)
| `Diffsel_bis -> `Diffsel_bis (Diffsel.diffsel ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~id:2)
......
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