# HG changeset patch
# User proteore
# Date 1536133836 14400
# Node ID 1c98865a8508f86af08877f22b45362879dcf024
# Parent  91b9b48d07b3158aa6eb72242da20696f0304511
planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty

diff -r 91b9b48d07b3 -r 1c98865a8508 GO-enrich.R
--- a/GO-enrich.R	Tue Aug 28 09:09:10 2018 -0400
+++ b/GO-enrich.R	Wed Sep 05 03:50:36 2018 -0400
@@ -1,8 +1,6 @@
-suppressMessages(library(clusterProfiler))
+suppressMessages(library(clusterProfiler,quietly = TRUE))
 
-#library(org.Sc.sgd.db)
-suppressMessages(library(org.Hs.eg.db))
-suppressMessages(library(org.Mm.eg.db))
+#library(org.Sc.sgd.db,quietly = TRUE)
 
 # Read file and return file content as data.frame
 readfile = function(filename, header) {
@@ -43,24 +41,29 @@
   ego<-enrichGO(gene=geneid,
                 universe=universe,
                 OrgDb=orgdb,
-                keytype="ENTREZID",
                 ont=ontology,
                 pAdjustMethod="BH",
                 pvalueCutoff=pval_cutoff,
                 qvalueCutoff=qval_cutoff,
                 readable=TRUE)
+  
   # Plot bar & dot plots
-  bar_name <- paste("EGO.", ontology, ".bar.png", sep = "")
-  png(bar_name)
-  p <- barplot(ego)
-  print(p)
-  dev.off()
-  dot_name <- paste("EGO.", ontology, ".dot.png", sep = "")
-  png(dot_name)
-  p <- dotplot(ego, showCategory=10)
-  print(p)
-  dev.off()
-  return(ego)
+  #if there are enriched GopTerms
+  if (length(ego$ID)>0){
+    bar_name <- paste("EGO.", ontology, ".bar.png", sep = "")
+    png(bar_name)
+    p <- barplot(ego)
+    print(p)
+    dev.off()
+    dot_name <- paste("EGO.", ontology, ".dot.png", sep = "")
+    png(dot_name)
+    p <- dotplot(ego, showCategory=10)
+    print(p)
+    dev.off()
+    return(ego)
+  } else {
+    warning(paste("No Go terms enriched (EGO) found for ",ontology,"ontology"),immediate. = TRUE,noBreaks. = TRUE,call. = FALSE)
+  }
 }
 
 check_ids <- function(vector,type) {
@@ -109,15 +112,17 @@
   names(args) <- argsDF$V1
   #print(args)
   
-  #save(args,file="args.Rda")
+  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
   #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
   
+  suppressMessages(library(args$species, character.only = TRUE, quietly = TRUE))
+  
   # Extract OrgDb
-  if (args$species=="human") {
+  if (args$species=="org.Hs.eg.db") {
     orgdb<-org.Hs.eg.db
-  } else if (args$species=="mouse") {
+  } else if (args$species=="org.Mm.eg.db") {
     orgdb<-org.Mm.eg.db
-  } else if (args$species=="rat") {
+  } else if (args$species=="org.Sc.eg.db") {
     orgdb<-org.Rn.eg.db
   }
 
@@ -149,7 +154,7 @@
     any(check_ids(input,"uniprot"))
     idFrom<-"UNIPROT"
     idTo<-"ENTREZID"
-    gene<-bitr(input, fromType=idFrom, toType=idTo, OrgDb=orgdb)
+    suppressMessages(gene<-bitr(input, fromType=idFrom, toType=idTo, OrgDb=orgdb))
     gene<-unique(gene$ENTREZID)
   } else if (id_type=="Entrez" & any(check_ids(input,"entrez"))) {
     gene<-unique(input)
@@ -193,7 +198,7 @@
       if (universe_id_type=="Uniprot" & any(check_ids(universe,"uniprot"))) {
         idFrom<-"UNIPROT"
         idTo<-"ENTREZID"
-        universe_gene<-bitr(universe, fromType=idFrom, toType=idTo, OrgDb=orgdb)
+        suppressMessages(universe_gene<-bitr(universe, fromType=idFrom, toType=idTo, OrgDb=orgdb))
         universe_gene<-unique(universe_gene$ENTREZID)
       } else if (universe_id_type=="Entrez" & any(check_ids(universe,"entrez"))) {
         universe_gene<-unique(universe)
diff -r 91b9b48d07b3 -r 1c98865a8508 cluster_profiler.xml
--- a/cluster_profiler.xml	Tue Aug 28 09:09:10 2018 -0400
+++ b/cluster_profiler.xml	Wed Sep 05 03:50:36 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="clusterProfiler" version="2018.08.28">
+<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.04">
     <description>
     GO terms classification and enrichment analysis
     </description>
@@ -7,7 +7,7 @@
         <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
         <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
         <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
-        <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
+        <requirement type="package" version="3.6.0">bioconductor-clusterprofiler</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         Rscript "$__tool_directory__/GO-enrich.R"
@@ -90,9 +90,9 @@
         </conditional>
             
         <param name="species" type="select" label="Select a species" >
-            <option value="human">Human</option>
-            <option value="mouse">Mouse</option>
-            <option value="rat">Rat</option>
+            <option value="org.Hs.eg.db">Human</option>
+            <option value="org.Mm.eg.db">Mouse</option>
+            <!--option value="org.Sc.eg.db">Rat</option-->
         </param>
         <conditional name="ggo">
             <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories representation analysis?"/>