# HG changeset patch
# User proteore
# Date 1537522546 14400
# Node ID 8f5025a35a84a61aa947c8bfebb7b766887f5eaa
# Parent  f325701409e6e96de113623bbabbbb22b78733b3
planemo upload commit 9d3e0b226140b566fc529fd0ffe7aa9e8388c6e5-dirty

diff -r f325701409e6 -r 8f5025a35a84 enrichment_v3.R
--- a/enrichment_v3.R	Wed Sep 19 09:23:51 2018 -0400
+++ b/enrichment_v3.R	Fri Sep 21 05:35:46 2018 -0400
@@ -30,9 +30,10 @@
 #	results file, barplot.png for the barplot image file and dotplot.png for the
 #	dotplot image file 
 
+options(warn=-1)  #TURN OFF WARNINGS !!!!!!
 
 # loading topGO library
-library(topGO)
+suppressMessages(library(topGO))
 
 # Read file and return file content as data.frame
 readfile = function(filename, header) {
@@ -88,6 +89,10 @@
     stop("Not enough/Too many arguments", call. = FALSE)
 }
 
+#save(options.args,file="/home/dchristiany/proteore_project/ProteoRE/tools/topGO/args.Rda")
+#load("/home/dchristiany/proteore_project/ProteoRE/tools/topGO/args.Rda")
+
+
 typeinput = options.args[1]
 listfile = options.args[2]
 onto = as.character(options.args[3])
@@ -348,16 +353,15 @@
 	
 		createDotPlot(cut_result, onto)
 	}
-  return(TRUE)
 }
 
 
 
 # Load R library ggplot2 to plot graphs
-library(ggplot2)
+suppressMessages(library(ggplot2))
 
 # Launch enrichment analysis
-allresult = goEnrichment(geneuniverse,sample,onto)
+allresult = suppressMessages(goEnrichment(geneuniverse,sample,onto))
 result = allresult[1][[1]]
 myGOdata = allresult[2][[1]]
 if (!is.null(result)){
diff -r f325701409e6 -r 8f5025a35a84 topGO.xml
--- a/topGO.xml	Wed Sep 19 09:23:51 2018 -0400
+++ b/topGO.xml	Fri Sep 21 05:35:46 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="topGO" name="topGO" version="2018.09.19">
+<tool id="topGO" name="topGO" version="2018.09.21">
     <description>
     Enrichment analysis for Gene Ontology
     </description>