# HG changeset patch
# User proteore
# Date 1537278595 14400
# Node ID ea5fecd4aa69641ba42cce47a7c6b24b5179196a
# Parent  b25f272d3505b07d5bce86d56c483c75b6df8641
planemo upload commit 229c140e131039467e2797f656d9acf916907dd7-dirty

diff -r b25f272d3505 -r ea5fecd4aa69 GO-enrich.R
--- a/GO-enrich.R	Tue Sep 18 09:20:27 2018 -0400
+++ b/GO-enrich.R	Tue Sep 18 09:49:55 2018 -0400
@@ -77,8 +77,6 @@
   #if there are enriched GopTerms
   if (length(ego$ID)>0){
     
-    print ('ego')
-    print (ego@result$Description)
     ego@result$Description <- sapply(ego@result$Description, function(x) {ifelse(nchar(x)>100, substr(x,1,100),x)},USE.NAMES = FALSE)
     nb_max_char = max_str_length_10_first(ego$Description)
     width = width_by_max_char(nb_max_char)
@@ -97,8 +95,9 @@
     p <- barplot(ego)
     print(p)
     dev.off()
+    
+    }
     return(ego)
-    }
   } else {
     warning(paste("No Go terms enriched (EGO) found for ",ontology,"ontology"),immediate. = TRUE,noBreaks. = TRUE,call. = FALSE)
   }
@@ -268,7 +267,7 @@
     if (args$go_enrich == "true") {
       ego<-enrich.GO(gene, universe_gene, orgdb, onto, pval_cutoff, qval_cutoff,plot)
       output_path = paste("cluster_profiler_EGO_",onto,".csv",sep="")
-      write.table(ego, output_path, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
+      write.table(ego, output_path, sep="\t", row.names = FALSE, quote=FALSE)
     }
   }
 }
diff -r b25f272d3505 -r ea5fecd4aa69 cluster_profiler.xml
--- a/cluster_profiler.xml	Tue Sep 18 09:20:27 2018 -0400
+++ b/cluster_profiler.xml	Tue Sep 18 09:49:55 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.18.3">
+<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.18.4">
     <description>
     GO terms classification and enrichment analysis
     </description>