Commit cbdf9bc0 authored by Philippe Veber's avatar Philippe Veber
Browse files

Multinomial: simplified output

parent ba5c6f77
......@@ -12,7 +12,7 @@ type result = [
| `Topological_LG of [`topological] dworkflow
| `Topological_WAG of [`topological] dworkflow
| `Tdg09 of [`tdg09] dworkflow
| `Multinomial of [`multinomial] dworkflow
| `Multinomial of text_file pworkflow
| `Msd of [`msd] dworkflow * float
]
......@@ -38,7 +38,7 @@ type dataset_res = {
plot_merged_results : svg pworkflow ;
}
let merge_results ?fna_infos ~res_by_tools () : text_file pworkflow =
let merge_results ?fna_infos ~(res_by_tools : result list) () : text_file pworkflow =
let fna_infos = match fna_infos with
| Some (sw) -> sw
| _ -> None
......@@ -54,7 +54,7 @@ let merge_results ?fna_infos ~res_by_tools () : text_file pworkflow =
| `Topological_LG d -> Topological.results d
| `Topological_WAG d -> Topological.results d
| `Tdg09 d -> Tamuri.results d
| `Multinomial d -> Multinomial.results d
| `Multinomial d -> d
| `Msd (d, _) -> Msd.results d
in
let opt = match res with
......
......@@ -11,7 +11,7 @@ type result = [
| `Topological_LG of [`topological] dworkflow
| `Topological_WAG of [`topological] dworkflow
| `Tdg09 of [`tdg09] dworkflow
| `Multinomial of [`multinomial] dworkflow
| `Multinomial of text_file pworkflow
| `Msd of [`msd] dworkflow * float
]
......
......@@ -3,17 +3,13 @@ open Bistro
open Bistro.Shell_dsl
open File_formats
let multinomial ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) : [`multinomial] dworkflow =
let multinomial ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) : text_file pworkflow =
let img = Env.env_py in
Workflow.shell ~descr:("calc_multinomial") [
mkdir_p dest;
cmd "python" ~img [
file_dump (string Scripts.calc_multinomial) ;
opt "-t" dep tree_sc;
opt "-a" dep faa;
opt "-o" ident (dest // "out.tsv") ;
opt "-o" ident dest ;
]
]
let results w =
Workflow.select w ["out.tsv"]
......@@ -109,7 +109,7 @@ let repo_of_detection_result res =
| `Topological_LG w -> item ["Topological_LG.results.tsv"] (Topological.results w)
| `Topological_WAG w -> item ["Topological_WAG.results.tsv"] (Topological.results w)
| `Tdg09 w -> item ["Tdg09.results.tsv"] (Tamuri.results w)
| `Multinomial w -> item ["Multinomial.results.tsv"] (Multinomial.results w)
| `Multinomial w -> item ["Multinomial.results.tsv"] w
| `Msd (w, e) -> item [sprintf "Msd.%f.results.tsv" e] (Msd.results w)
] ;
[
......
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