Commit e9b996b3 authored by Carine Rey's avatar Carine Rey Committed by Philippe Veber
Browse files

add model in descr in pcoc and tdg09

parent 0e43ad72
......@@ -5,8 +5,8 @@ open File_formats
let img = [ docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"08312018" () ]
let pcoc ?plot_complete ?gamma ?catx_est ~(faa:aminoacid_fasta pworkflow) ~(tree:_ workflow) : [`pcoc] dworkflow =
Workflow.shell ~descr:"convergence_detection.pcoc" [
let pcoc ?(descr = "") ?plot_complete ?gamma ?catx_est ~(faa:aminoacid_fasta pworkflow) ~(tree:_ workflow) : [`pcoc] dworkflow =
Workflow.shell ~descr:("convergence_detection.pcoc."^descr) [
cmd "pcoc_det.py" ~img [
opt "-t" dep tree;
opt "-m" string "-";
......
......@@ -4,6 +4,7 @@ open File_formats
val img : Shell_dsl.container_image list
val pcoc :
?descr:string ->
?plot_complete:bool ->
?gamma:bool ->
?catx_est:int ->
......
......@@ -202,11 +202,11 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
let n_cycles = if preview then 2000 else 2000 in
let seed = Hashtbl.hash dataset.seed in
match det_meth with
| `Pcoc -> `Pcoc (Pcoc.pcoc ~catx_est:10 ~plot_complete:false ~gamma:false ~faa ~tree:tree_sc)
| `Pcoc_gamma -> `Pcoc_gamma (Pcoc.pcoc ~catx_est:10 ~plot_complete: false ~gamma:true ~faa ~tree:tree_sc)
| `Pcoc_C60 -> `Pcoc_C60 (Pcoc.pcoc ~catx_est:60 ~plot_complete: false ~gamma:false ~faa ~tree:tree_sc)
| `Tdg09 -> `Tdg09 (Tamuri.tdg09 ~faa ~tree:tree_sc)
| `Diffsel -> `Diffsel (Diffsel.diffsel ~descr ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~seed ())
| `Pcoc -> `Pcoc (Pcoc.pcoc ~descr ~catx_est:10 ~plot_complete:false ~gamma:false ~faa ~tree:tree_sc)
| `Pcoc_gamma -> `Pcoc_gamma (Pcoc.pcoc ~descr ~catx_est:10 ~plot_complete: false ~gamma:true ~faa ~tree:tree_sc)
| `Pcoc_C60 -> `Pcoc_C60 (Pcoc.pcoc ~descr ~catx_est:60 ~plot_complete: false ~gamma:false ~faa ~tree:tree_sc)
| `Tdg09 -> `Tdg09 (Tamuri.tdg09 ~descr ~faa ~tree:tree_sc)
| `Diffsel -> `Diffsel (Diffsel.diffsel ~descr ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~id:1 ~seed ())
| `Identical_LG -> `Identical_LG (Identical.identical ~faa ~tree_id ~tree_sc ~prot_model:"LG08")
| `Identical_WAG -> `Identical_WAG (Identical.identical ~faa ~tree_id ~tree_sc ~prot_model:"WAG01")
| `Topological_LG -> `Topological_LG (Topological.topological ~faa ~tree:tree_id ~tree_conv ~prot_model:"LG08")
......
......@@ -5,13 +5,13 @@ open File_formats
let img = Env.env_tdg09
let tdg09 ~(faa:aminoacid_fasta pworkflow) ~(tree:_ pworkflow) : [`tdg09] dworkflow =
let tdg09 ?(descr="") ~(faa:aminoacid_fasta pworkflow) ~(tree:_ pworkflow) : [`tdg09] dworkflow =
let tdg09_out = dest // "tdg09.yaml" in
let tmp_ali_phy = dest // "tmp_ali.phy" in
let tmp_tree = dest // "tmp.nw" in
let package = tmp // "diffsel_script_utils.py" in
let script = tmp // "try_again.py" in
Workflow.shell ~descr:"convergence_detection.run_tdg09" [
Workflow.shell ~descr:("convergence_detection.run_tdg09."^descr) [
within_container img (
and_list [
mkdir_p dest ;
......
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