# HG changeset patch
# User proteore
# Date 1537360909 14400
# Node ID 81d204aac06bce4ccacb48d75b65a4573cc4710b
# Parent  fdc8fbfbfcbcd68fd1449346653778f7b29ad10a
planemo upload commit 26575daf6b3f9ed4f203b50e10e58933b94a94c5-dirty

diff -r fdc8fbfbfcbc -r 81d204aac06b enrichment_v3.R
--- a/enrichment_v3.R	Fri Sep 14 08:54:43 2018 -0400
+++ b/enrichment_v3.R	Wed Sep 19 08:41:49 2018 -0400
@@ -63,7 +63,6 @@
 
 
 # Parse command line arguments
-
 args = commandArgs(trailingOnly = TRUE)
 
 # create a list of the arguments from the command line, separated by a blank space
@@ -88,6 +87,9 @@
     stop("Not enough/Too many arguments", call. = FALSE)
 }
 
+#save(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])
diff -r fdc8fbfbfcbc -r 81d204aac06b topGO.xml
--- a/topGO.xml	Fri Sep 14 08:54:43 2018 -0400
+++ b/topGO.xml	Wed Sep 19 08:41:49 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="topGO" name="topGO" version="2018.09.14">
+<tool id="topGO" name="topGO" version="2018.09.18">
     <description>
     Enrichment analysis for Gene Ontology
     </description>
@@ -10,7 +10,7 @@
         <requirement type="package" version="3.5.0">bioconductor-org.ce.eg.db</requirement>
         <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement>
         <requirement type="package" version="3.5.0">bioconductor-org.sc.sgd.db</requirement>
-        <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement-->
+        <requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement>
         <requirement type="package" version="1.56.0">bioconductor-graph</requirement>
         <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
         <requirement type="package" version="3.5.0">bioconductor-go.db</requirement>
@@ -78,7 +78,7 @@
     </when>
     <when value="file_all">
       <param name="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>
-      <param name="column" type="text" label="Please specify the column where you would like to apply the comparison (e.g : Enter c1)" value="c1"/> 
+      <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter "c1" for column n°1..)" value="c1"/> 
     
       <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> 
  	<option value="TRUE" selected="true">Yes</option>
@@ -87,12 +87,12 @@
     </when>
   </conditional>
       <param name="geneuniverse" type="select" label="Select a specie">
-        <!--option value="org.At.tair.db" >Arabidopsis</option-->
-        <option value="org.Ce.eg.db" >C.elegans</option>
-        <option value="org.Dm.eg.db" >Fly</option>
-        <option value="org.Hs.eg.db" selected="true">Human</option>
-        <option value="org.Mm.eg.db" >Mouse</option>
-        <option value="org.Sc.sqd.db" >Yeast</option>
+        <option value="org.At.tair.db" >Arabidopsis</option>
+        <option value="org.Ce.eg.db" >Worm (C.elegans)</option>
+        <option value="org.Dm.eg.db" >Fly (D. melanogaster)</option>
+        <option value="org.Hs.eg.db" selected="true">Human (H. sapiens)</option>
+        <option value="org.Mm.eg.db" >Mouse (M. musculus)</option>
+        <option value="org.Sc.sgd.db" >Yeast (S. cerevisiae)</option>
       </param>
 
       <param name="ontocat" type="select" label="Ontology category">