# HG changeset patch
# User proteore
# Date 1561623745 14400
# Node ID 79d0f1773124e758948ffad451122badcc2dc99d
# Parent  537a0aae9b41982cc9a8387847bfc333f3e0321c
planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty

diff -r 537a0aae9b41 -r 79d0f1773124 topGO.xml
--- a/topGO.xml	Mon Jun 03 11:35:10 2019 -0400
+++ b/topGO.xml	Thu Jun 27 04:22:25 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.06.01">
+<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.06.27">
     <description>(Human, Mouse, Rat)[topGO]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -51,7 +51,7 @@
 
     <inputs>
   <conditional name="inputtype">
-    <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene only)" help="Copy/paste or from a file">
+    <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene Id)" help="Copy/paste or from a file">
       <option value="file" selected="true">Input file containing your IDs</option>
       <option value="copy_paste">Copy/paste your list of IDs</option> 
     </param>
@@ -76,7 +76,7 @@
     </when>
   </conditional>
   <conditional name="background_genes">
-    <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs ?"/>
+    <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Use your own background (ID list) ?"/>
     <when value="true">
       <conditional name="inputtype">
         <param name="filetype" type="select" label="Enter your background IDs (Ensembl gene IDs)" help="(e.g : ENSG00000139618)">
@@ -106,7 +106,7 @@
     </when>
     <when value="false"/>
   </conditional>
-    <param name="geneuniverse" type="select" label="Species">
+    <param name="geneuniverse" type="select" label="Species (human, mouse, rat)">
       <!--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-->
@@ -120,7 +120,7 @@
       <option value="CC" >Cellular Component</option>
       <option value="MF" >Molecular Function</option>
     </param>
-    <param name="option" type="select" label="Select the topGO parameter (see user doc)">
+    <param name="option" type="select" label="Select GO scoring method (read user doc section)">
       <option value="classic" >Classic Fisher test</option>
       <option value="elim" selected="true">Elim</option>
       <option value="weight01" >Weight01</option>
@@ -202,7 +202,7 @@
  
 "GO terms category": select either Biogical Process (BP)(by default), Cellular Component (CC) or Molecular Function (MF)
  
-"Select the topGO parameter (see user doc)": topGO provides a classic Fisher test for evaluating which GO terms are over-represented in your gene/protein list; other methodologies are also provided (Elim, Weight01, Parentchild). For the merits of each option and their algorithmic descriptions, please refer to topGO manual: 
+"Select GO scoring method: topGO provides the commonly used Fisher test for evaluating which GO terms are over-represented in your gene/protein list; it also provides other GO scoring algorithms (i.e. Elim, Weight01, Parentchild). For the merits of each option and their algorithmic description, please refer to topGO manual: 
 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
 
 "p-value threshold (e.g : 1e-3)": must be in the form of "1e-5" (i.e. 0.00001)
@@ -214,7 +214,7 @@
 
 **Output**
 
-Three outputs are available : a textual output, a barplot and/or a dotplot (set by default) graphical outputs. 
+Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)). 
 
 *Textual output*
 
@@ -259,13 +259,13 @@
 
 **Galaxy integration**
 
-Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+Lisa Perus, Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
 
 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
 
-Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+Help: contact@proteore.org for any questions or concerns about this tool.
 
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    <citations>