Commit 0ab84680 authored by Sebastien Theil's avatar Sebastien Theil
Browse files

Add ncpu option.

parent a5cce309
......@@ -8,6 +8,7 @@
#' @param verbose Verbose level. (1: quiet, 3: verbal)
#' @param confidence Bootstrap threshold 0...100
#' @param returnval Boolean to return values in console or not.
#' @param ncpu Number of cpus to use.
#'
#'
#' @return Return a taxonomy table with multiple ancestor checking and incongruence checking when 2 databases are used.
......@@ -22,7 +23,7 @@
assign_taxo_fun <- function(dada_res = dada_res, output = "./idtaxa/", id_db = "/PathToDB/UNITE_idtaxa.Rdata", confidence = 50, verbose = 1, returnval = TRUE){
assign_taxo_fun <- function(dada_res = dada_res, output = "./idtaxa/", id_db = "/PathToDB/UNITE_idtaxa.Rdata", confidence = 50, verbose = 1, returnval = TRUE, ncpu=NULL){
if(verbose == 3){
......@@ -47,7 +48,7 @@ assign_taxo_fun <- function(dada_res = dada_res, output = "./idtaxa/", id_db =
taxid_list=vector("list", length(db_list)+1)
for (i in 1:length(db_list)){
db_file <- db_list[i]
taxid_list[[i]] <- idTaxa_assign(db_file, dna, colnames(dada_res$seqtab.export), confidence)
taxid_list[[i]] <- idTaxa_assign(db_file, dna, colnames(dada_res$seqtab.export), confidence, ncpu)
}
if(verbose == 3){
......
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