add option plot_all_sites in plot_merge_results

lib/convergence_detection.ml

@@ -73,8 +73,7 @@ let merge_results ~res_by_tools : text_file workflow =
   ]
 
 
-let plot_merge_results ~(res_by_tools:result list) ~tree ~faa ~tsv : svg workflow =
-  let plot_all_sites = true in
+let plot_merge_results ~plot_all_sites ~(res_by_tools:result list) ~tree ~faa ~tsv : svg workflow =
   (*let env = docker_image ~account:"carinerey" ~name:"ete3" ~tag:"3.0.0b35" () in*)
   let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"06212018" () in
   (* use of pcoc env due to its working X server for dra plot with ete3 *)

lib/convergence_detection.mli

@@ -33,6 +33,7 @@ val merge_results :
   text_file workflow
 
 val plot_merge_results :
+    plot_all_sites: bool ->
     res_by_tools : result list ->
     tree:nhx workflow ->
     faa:aminoacid_fasta workflow ->

lib/pipeline.ml

@@ -184,7 +184,7 @@ let derive_from_dataset ~dataset ~preview =
   let tsv = merged_results in
   let faa = dataset.dataset.faa in
   let tree = Tree_dataset.tree dataset.dataset.tree_dataset `Detection in
-  let plot_merged_results = plot_merge_results ~res_by_tools ~tsv ~faa ~tree in
+  let plot_merged_results = plot_merge_results ~plot_all_sites:true ~res_by_tools ~tsv ~faa ~tree in
   let model_prefix = dataset.model_prefix in
   let tree_prefix = dataset.tree_prefix in
   {model_prefix; tree_prefix; res_by_tools ; merged_results ; plot_merged_results}