Commit 1238ccc7 authored by LANORE Vincent's avatar LANORE Vincent
Browse files

Identation + removed empty lines in identical.ml

parent 2439efc1
......@@ -4,12 +4,9 @@ open Bistro.EDSL
open Bistro_bioinfo.Std
open File_formats
let assign k v =
seq ~sep:"=" [ string k ; v ]
let conf_file_bppml ~tree ~faa ~out ~config =
seq ~sep:"\n" (
[
......@@ -45,13 +42,12 @@ let bppml ?(descr="") ~faa ~tree ~config : _ workflow =
mkdir_p dest;
cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppml ~tree ~faa ~out ~config ))];
cmd "bppml" [
assign "param" config_f;
]
assign "param" config_f;
]
]
)
]
let conf_file_bppancestor ~tree ~faa ~out ~config =
seq ~sep:"\n" (
[
......@@ -76,7 +72,6 @@ let conf_file_bppancestor ~tree ~faa ~out ~config =
@ config
)
let bppancestor ?(descr="") ~faa ~tree ~config : _ workflow =
let env = docker_image ~account:"carinerey" ~name:"bppsuite" ~tag:"07052018" () in
let config_f = dest // "config_bppancestor.bpp" in
......@@ -87,13 +82,12 @@ let bppancestor ?(descr="") ~faa ~tree ~config : _ workflow =
mkdir_p dest;
cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppancestor ~tree ~faa ~out ~config))];
cmd "bppancestor" [
assign "param" config_f;
]
assign "param" config_f;
]
]
)
]
let identical ~(tree_id:_ workflow) ~(tree_sc:_ workflow) ~(faa:aminoacid_fasta workflow) ~prot_model : [`identical] directory workflow =
let config = [assign "model" (string prot_model)] in
let out1 = dest // "out1.tsv" in
......@@ -105,16 +99,14 @@ let identical ~(tree_id:_ workflow) ~(tree_sc:_ workflow) ~(faa:aminoacid_fasta
workflow ~descr:("identical."^prot_model) [
mkdir dest ;
cmd "python" ~env [
file_dump (string Scripts.calc_identical) ;
opt "-t" dep tree_sc;
opt "-a" dep faa;
opt "-p" dep proba;
opt "-o" ident out1 ;
opt "-o2" ident out2 ;
file_dump (string Scripts.calc_identical) ;
opt "-t" dep tree_sc;
opt "-a" dep faa;
opt "-p" dep proba;
opt "-o" ident out1 ;
opt "-o2" ident out2 ;
]
]
let results run_identical : text_file workflow =
run_identical / selector ["out1.tsv"]
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment