--- a/topGO.xml	Fri Sep 21 05:35:46 2018 -0400
+++ b/topGO.xml	Mon Oct 15 11:30:04 2018 -0400
@@ -1,7 +1,5 @@
-<tool id="topGO" name="topGO" version="2018.09.21">
-    <description>
-    Enrichment analysis for Gene Ontology
-    </description>
+<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.10.12">
+    <description>(Human, Mouse, Rat) (topGO)</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
         <requirement type="package" version="3.0.0">r-ggplot2</requirement>
@@ -20,48 +18,31 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-    
-  #if $inputtype.filetype == "file_all": 
-  Rscript --vanilla $__tool_directory__/enrichment_v3.R 
-  --inputtype tabfile 
-  --input '$inputtype.genelist' 
-  --ontology '$ontocat' 
-  --option '$option' 
-  --threshold '$threshold' 
-  --correction '$correction' 
-  --textoutput '$condtext.textoutput' 
-  --barplotoutput '$condbar.barplotoutput' 
-  --dotplotoutput '$conddot.dotplotoutput' 
-  --column '$inputtype.column' 
-  --geneuniverse '$geneuniverse' 
-  --header '$inputtype.header'
-  #end if
-    
-    
-  #if $inputtype.filetype == "copy_paste": 
-  Rscript --vanilla $__tool_directory__/enrichment_v3.R 
-  --inputtype copypaste 
-  --input '$inputtype.genelist' 
-  --ontology '$ontocat' 
-  --option '$option' 
-  --threshold '$threshold' 
-  --correction '$correction' 
-  --textoutput '$condtext.textoutput' 
-  --barplotoutput '$condbar.barplotoutput' 
-  --dotplotoutput '$conddot.dotplotoutput' 
-  --column c1 
-  --geneuniverse '$geneuniverse' 
-  --header None
+       
+  Rscript --vanilla $__tool_directory__/topGO_enrichment.R 
+  --inputtype="$inputtype.filetype"
+  --input='$inputtype.genelist'
+
+  #if $inputtype.filetype == "file"
+    --column='$inputtype.column'
+    --header='$inputtype.header'
   #end if
 
-
+  --ontology='$ontocat'
+  --option='$option'
+  --threshold='$threshold'
+  --correction='$correction'
+  --textoutput='$textoutput'
+  --barplotoutput='$barplot'
+  --dotplotoutput='$dotplot'
+  --geneuniverse='$geneuniverse' 
 
     ]]></command>
 
     <inputs>
   <conditional name="inputtype">
     <param name="filetype" type="select" label="Select your type of input file" help="The identifiers must be Ensembl gene IDs (e.g : ENSG00000139618). If it is not the case, please use the ID Mapping tool.">
-      <option value="file_all" selected="true">Input file containing your identifiers</option>
+      <option value="file" selected="true">Input file containing your identifiers</option>
       <option value="copy_paste">Copy/paste your list of IDs</option> 
     </param>
     <when value="copy_paste">
@@ -76,85 +57,58 @@
         </sanitizer>
       </param>
     </when>
-    <when value="file_all">
+    <when value="file">
       <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 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>
-        <option value="FALSE" selected="false">No</option>
-      </param>
+      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file have a header?" /> 
     </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" >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">
-              <option value="BP" >Biological Process</option>
-              <option value="CC" >Cellular Component</option>
-              <option value="MF" >Molecular Function</option>
-        </param>
-
-        <param name="option" type="select" label="Choose the topGO option for your analysis">
-                <option value="classic" >Classic fisher test</option>
-                <option value="elim" selected="true">Elim</option>
-                <option value="weight01" >Weight01</option>
-                <option value="parentchild" >ParentChild</option>
-          </param>
-        <param name="threshold" type="text" label="Enter the p-value threshold level under the form 1e-level wanted (e.g : 1e-3)" value="1e-3"/>
-	<param name="correction" label="Choose a correction for multiple testing" type="select">
-             <option value="none" >None</option>
-             <option value="holm">Holm correction</option>
-             <option value="hochberg" >Hochberg correction</option>
-             <option value="hommel" >Hommel correction</option>
-             <option value="bonferroni" >Bonferroni correction</option>
-             <option value="BH" selected="true">Benjamini and Hochberg</option>
-             <option value="BY" >Benjamini and Yekutieli</option>
-             <option value="fdr" >FDR</option>
-           </param>
-            <conditional name="condtext">
-            <param name="textoutput" type="select" label="Generate a text file for results">
-              <option value="TRUE">Yes</option>
-              <option value="FALSE">No</option>
-            </param>
-            <when value="TRUE"/>
-            <when value="FALSE"/>
-          </conditional>
-          <conditional name="condbar">
-            <param name="barplotoutput" type="select" label="Generate a barplot of over-represented GO terms">
-              <option value="TRUE">Yes</option>
-              <option value="FALSE">No</option>
-            </param>
-            <when value="TRUE"/>
-            <when value="FALSE"/>
-          </conditional>
-          <conditional name="conddot">
-              <param name="dotplotoutput" type="select" label="Generate a dotplot of over-represented GO terms">
-              <option value="TRUE">Yes</option>
-              <option value="FALSE">No</option>
-            </param>
-            <when value="TRUE"/>
-            <when value="FALSE"/>
-          </conditional>
+    <param name="geneuniverse" type="select" label="Select a specie">
+      <!--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">
+      <option value="BP" >Biological Process</option>
+      <option value="CC" >Cellular Component</option>
+      <option value="MF" >Molecular Function</option>
+    </param>
+    <param name="option" type="select" label="Choose the topGO option for your analysis">
+      <option value="classic" >Classic fisher test</option>
+      <option value="elim" selected="true">Elim</option>
+      <option value="weight01" >Weight01</option>
+      <option value="parentchild" >ParentChild</option>
+    </param>
+    <param name="threshold" type="text" label="Enter the p-value threshold level under the form 1e-level wanted (e.g : 1e-3)" value="1e-3"/>
+	  <param name="correction" label="Choose a correction for multiple testing" type="select">
+      <option value="none" >None</option>
+      <option value="holm">Holm correction</option>
+      <option value="hochberg" >Hochberg correction</option>
+      <option value="hommel" >Hommel correction</option>
+      <option value="bonferroni" >Bonferroni correction</option>
+      <option value="BH" selected="true">Benjamini and Hochberg</option>
+      <option value="BY" >Benjamini and Yekutieli</option>
+      <option value="fdr" >FDR</option>
+    </param>
+    <param name="textoutput" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a text file for results" />
+    <param name="barplot" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a barplot of over-represented GO terms" />
+    <param name="dotplot" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a dotplot of over-represented GO terms" />
     </inputs>
     <outputs>
 
-      <data name="outputtext" format="tabular" label="Text output for topGO analysis $ontocat category" from_work_dir="result.csv">
-        <filter>condtext['textoutput']=="TRUE"</filter>
+      <data name="outputtext" format="tsv" label="Text output for topGO analysis $ontocat category" from_work_dir="result">
+        <filter>textoutput</filter>
       </data>
 
       <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
-        <filter>condbar['barplotoutput']=="TRUE"</filter>
+        <filter>barplot</filter>
       </data>
       
       <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png">
-        <filter>conddot['dotplotoutput']=="TRUE"</filter>
+        <filter>dotplot</filter>
       </data>
       
    </outputs>