# HG changeset patch
# User proteore
# Date 1545382525 18000
# Node ID b62fd03a3822fb11d7ed3279a3caa9fcb53fd34e
# Parent  eb12bb18b5dd10efc8fe9b9885129a9f40483ee0
planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty

diff -r eb12bb18b5dd -r b62fd03a3822 GO-enrich.R
--- a/GO-enrich.R	Tue Dec 18 03:21:33 2018 -0500
+++ b/GO-enrich.R	Fri Dec 21 03:55:25 2018 -0500
@@ -152,13 +152,14 @@
   argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
   args <- as.list(as.character(argsDF$V2))
   names(args) <- argsDF$V1
+  
+  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
+  
   plot = unlist(strsplit(args$plot,","))
   go_represent=str2bool(args$go_represent)
   go_enrich=str2bool(args$go_enrich)
   
-  #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
@@ -232,7 +233,7 @@
         # Get file content
         universe_file = read_file(universe_filename, universe_header)
         # Extract Protein IDs list
-        universe <- sapply(universe_file[,universe_ncol], function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE)
+        universe <- unlist(sapply(universe_file[,universe_ncol], function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
       }
       universe_id_type = args$universe_id_type
       ##to initialize
diff -r eb12bb18b5dd -r b62fd03a3822 cluster_profiler.xml
--- a/cluster_profiler.xml	Tue Dec 18 03:21:33 2018 -0500
+++ b/cluster_profiler.xml	Fri Dec 21 03:55:25 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.18">
+<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.21">
     <description>(Human, Mouse, Rat)[clusterProfiler]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -204,16 +204,15 @@
                 <element name="cluster_profiler_EGO_CC.csv" file="cluster_profiler_EGO_CC.csv" ftype="csv"/>
                 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_EGO_BP.csv" ftype="csv"/>
                 <element name="cluster_profiler_EGO_MF.csv" file="cluster_profiler_EGO_MF.csv" ftype="csv"/>
-
             </output_collection>
             <output_collection name="graph_output">
-                <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png" diff="size"/>
-                <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png" diff="size"/>
-                <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png" diff="size"/>
-                <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png" diff="size"/>
-                <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png" diff="size"/>
-                <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png" diff="size"/>
-                <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png" diff="size"/>
+                <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/>
+                <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/>
+                <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/>
+                <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png"/>
+                <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png"/>
+                <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png"/>
+                <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png"/>
             </output_collection>
         </test>
     </tests>
@@ -231,7 +230,7 @@
 
 -----
 
-**Input **
+**Input**
 
 Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) or by copy/pasting your IDs (separated by a space).