# HG changeset patch
# User proteore
# Date 1583140985 0
# Node ID a4db9efe1e430a515d800e0ab47058c25a5d99ad
# Parent  9ac0ade20b3f3f5cda80a960da09c11eed79c006
"planemo upload commit 78a50fa16dcea6afd93a2f4de17ed193a2aa7dd3-dirty"

diff -r 9ac0ade20b3f -r a4db9efe1e43 kegg_maps_visualization.R
--- a/kegg_maps_visualization.R	Wed Jan 08 09:03:41 2020 +0000
+++ b/kegg_maps_visualization.R	Mon Mar 02 09:23:05 2020 +0000
@@ -177,6 +177,15 @@
   return(c(min,max))
 }
 
+check_pathway_ids<- function(pathways_ids) {
+  problematic_pathways <- c("04215","04723")
+  to_remove <- intersect(pathways_ids,problematic_pathways)
+  if (length(to_remove) > 0){ print(paste("Pathway(s)",to_remove,"have been remove from input")) }
+  pathways_ids <- pathways_ids[which(!pathways_ids %in% problematic_pathways)]
+  if (length(pathways_ids) == 0){stop("No pathways ids to process")}
+  return (pathways_ids)
+}
+
 get_args <- function(){
   
   ## Collect arguments
@@ -238,7 +247,7 @@
     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"] }
+  if (args$native_kegg) {ids = check_pathway_ids(ids)} #remove problematic pathways
   pathways_list <- read_file(args$pathways_list,F)
   if (!is.null(args$id_list)) {
     id_list <- get_list_from_cp(args$id_list)
diff -r 9ac0ade20b3f -r a4db9efe1e43 kegg_maps_visualization.xml
--- a/kegg_maps_visualization.xml	Wed Jan 08 09:03:41 2020 +0000
+++ b/kegg_maps_visualization.xml	Mon Mar 02 09:23:05 2020 +0000
@@ -1,9 +1,10 @@
-<tool id="kegg_maps_visualization" name="Pathways visualization" version="2020.01.08">
-    <description>of (differentially expressed) genes/proteins [KEGG]</description>
+<tool id="kegg_maps_visualization" name="KEGG pathways mapping and visualization" version="2020.03.02">
+    <description>[PathView]</description>
     <requirements>
         <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>
+        <requirement type="package" version="1.30.10">r-biocmanager</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         Rscript $__tool_directory__/kegg_maps_visualization.R 
@@ -261,6 +262,11 @@
 2. "Select ID type for genes to map on the pathway(s)": Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number. IDs to be mapped can be either provided by copy/paste or a file (tabular, tsv, txt) with a column containing the IDs. 
 3. "Map quantitative data on the pathway ?": Yes/No (default is No). Fold change values (up to three columns) from a dataset (same file as identifiers to map) can be graphically represented on the final figure (using a range of color representing the fold-change values).
 
+.. class:: warningmark 
+
+Some pathway ids causes error with the KEGG API: **hsa04215**, **mmu04723**. These ids will not be used if present in input.
+
+
 Below is an example of an input file with identifiers (uniprot_AC) and fold_change values.
 
 .. csv-table:: Simulated data