Commit bc1d0938 authored by Carine Rey's avatar Carine Rey Committed by Philippe Veber
Browse files

add --max_gap_allowed --max_gap_allowed_in_conv_leaves

parent 8be41188
......@@ -5,7 +5,7 @@ open File_formats
let img = [ docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"08312018" () ]
let pcoc ?(descr = "") ?plot_complete ?gamma ?catx_est ~(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 pworkflow) ~(tree:_ workflow) (): [`pcoc] dworkflow =
Workflow.shell ~descr:("convergence_detection.pcoc."^descr) [
cmd "pcoc_det.py" ~img [
opt "-t" dep tree;
......@@ -14,6 +14,8 @@ let pcoc ?(descr = "") ?plot_complete ?gamma ?catx_est ~(faa:aminoacid_fasta pw
opt "-o" ident dest ;
option ( flag string "--gamma" ) gamma;
option ( opt "-CATX_est" int) catx_est;
option ( opt "--max_gap_allowed" int) max_gap_per_pos;
option ( opt "--max_gap_allowed_in_conv_leaves" int) max_gap_per_conv_leaf;
option ( flag string "--plot --plot_complete_ali" ) plot_complete;
]
]
......
......@@ -8,8 +8,11 @@ val pcoc :
?plot_complete:bool ->
?gamma:bool ->
?catx_est:int ->
?max_gap_per_pos:int ->
?max_gap_per_conv_leaf:int ->
faa:aminoacid_fasta pworkflow ->
tree:_ pworkflow ->
unit ->
[`pcoc] dworkflow
val results :
......
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