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Commit 5e8aa074 authored by Philippe Veber's avatar Philippe Veber

RERconverge: don't use master_tree and add keep_ident to iqtree invocation

parent 30b9a1dd
......@@ -632,7 +632,9 @@ let rer_converge ?max_read ?transform ?weighted ?scale ?continuous ~db
let clipped_tree =
clip_tree_on_alignment ~handle_tags:false species_tree q
in
Iqtree.iqtree ~te:clipped_tree (*~m:model*) ~st:`DNA ~spp
Iqtree.iqtree
~keep_ident:true ~te:clipped_tree
(*~m:model*) ~st:`DNA ~spp
(`phylip q)
|> Iqtree.treefile)
ali_files
......@@ -641,4 +643,4 @@ let rer_converge ?max_read ?transform ?weighted ?scale ?continuous ~db
let gene_tree_set = RER.gene_tree_file gene_trees in
let phenotype = RER.phenotypes_of_convergent_species phenotypes in
RER.rer_converge ?max_read ?transform ?weighted ?scale ?continuous
~min_specs:10 ~gene_tree_set ~phenotype ~master_tree:species_tree
~min_specs:10 ~gene_tree_set ~phenotype
......@@ -42,7 +42,7 @@ let ropt f =
Option.value_map ~f ~default:(string "NA")
let script ?max_read ?min_specs ~transform ~weighted ~scale ~continuous ~gene_tree_set
~phenotype ~master_tree =
~phenotype (* ~master_tree *) =
let max_read = ropt int max_read in
let min_specs = ropt int min_specs in
[%script
......@@ -53,12 +53,11 @@ suppressPackageStartupMessages({
library(RERconverge)
})
masterTree <- read.tree(file="{{dep master_tree}}")
gene_trees <- readTrees("{{dep gene_tree_set}}", max.read={{max_read}}, masterTree=masterTree, minSpecs={{min_specs}})
#masterTree <- read.tree(file="{dep master_tree}")
gene_trees <- readTrees("{{dep gene_tree_set}}", max.read={{max_read}}, minSpecs={{min_specs}})
relative_rates <- getAllResiduals(
gene_trees,
useSpecies = useSpecies,
transform = "{{template_transform transform}}",
weighted = {{template_bool weighted}},
scale = {{template_bool scale}}
......@@ -118,7 +117,7 @@ write_tsv("{{dest}}", res)
|}]
let rer_converge ?max_read ?min_specs ?(transform = `sqrt) ?(weighted = true)
?(scale = true) ?(continuous = false) ~master_tree ~gene_tree_set ~phenotype =
?(scale = true) ?(continuous = false) (* ~master_tree *) ~gene_tree_set ~phenotype =
Bistro_utils.R_script.workflow ~img ~descr:"rer_converge"
(script ?max_read ~transform ~weighted ~scale ~continuous
?min_specs ~gene_tree_set ~phenotype ~master_tree)
?min_specs ~gene_tree_set ~phenotype (* ~master_tree *))
......@@ -13,7 +13,7 @@ val rer_converge :
?weighted:bool ->
?scale:bool ->
?continuous:bool ->
master_tree:newick file ->
(* master_tree:newick file -> *)
gene_tree_set:tsv file ->
phenotype:tsv file ->
tsv file
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