# HG changeset patch
# User proteore
# Date 1579105863 18000
# Node ID 8e611bdc96ecff4dafd36c0bcf47f4c4e7a3b615
# Parent  dfceadc0b703e89500ee04e0ce22d79f2abfea81
"planemo upload commit 6bef056b0e52bfa39dbe8591bfe67f8c95bf3ba2-dirty"

diff -r dfceadc0b703 -r 8e611bdc96ec kegg_maps_visualization.R
--- a/kegg_maps_visualization.R	Fri Jun 28 05:16:30 2019 -0400
+++ b/kegg_maps_visualization.R	Wed Jan 15 11:31:03 2020 -0500
@@ -85,8 +85,8 @@
 
 get_ref_pathways <- function(species){
   ##all available pathways for the species
-  pathways <-keggLink("pathway", species)
-  tot_path<-unique(pathways)
+  pathways <- keggLink("pathway", species)
+  tot_path <- unique(pathways)
   
   ##formating the dat into a list object
   ##key= pathway ID, value = genes of the pathway in the kegg format
@@ -238,6 +238,7 @@
     pathways_file = read_file(args$pathways_input,header2)
     ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
   }
+  if (args$native_kegg) { ids <- ids[ids != "04215"] }
   pathways_list <- read_file(args$pathways_list,F)
   if (!is.null(args$id_list)) {
     id_list <- get_list_from_cp(args$id_list)
diff -r dfceadc0b703 -r 8e611bdc96ec kegg_maps_visualization.xml
--- a/kegg_maps_visualization.xml	Fri Jun 28 05:16:30 2019 -0400
+++ b/kegg_maps_visualization.xml	Wed Jan 15 11:31:03 2020 -0500
@@ -1,8 +1,9 @@
-<tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.06.27.1">
+<tool id="kegg_maps_visualization" name="Pathways visualization" version="2020.01.08">
     <description>of (differentially expressed) genes/proteins [KEGG]</description>
     <requirements>
-        <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
-        <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
+        <requirement type="package" version="3.6.2" >R</requirement>
+        <requirement type="package" version="1.26.0">bioconductor-pathview</requirement>
+        <requirement type="package" version="1.26.0">bioconductor-keggrest</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         Rscript $__tool_directory__/kegg_maps_visualization.R