# HG changeset patch
# User proteore
# Date 1561622805 14400
# Node ID 51d79e4496cc1a3f434f1b5c35033c77e77a0b56
# Parent  6a0d0b5b91f2b458d0337e88669470bdc6ae060f
planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty

diff -r 6a0d0b5b91f2 -r 51d79e4496cc cluster_profiler.xml
--- a/cluster_profiler.xml	Mon Jun 03 09:52:08 2019 -0400
+++ b/cluster_profiler.xml	Thu Jun 27 04:06:45 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.06.01.1">
+<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.06.27">
     <description>(Human, Mouse, Rat)[clusterProfiler]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -56,7 +56,7 @@
     ]]></command>
     <inputs>
         <conditional name="input" >
-            <param name="ids" type="select" label="Enter your IDs (UniProt Accession numer or Gene ID)" help="Copy/paste or from a file (e.g. table)" >
+            <param name="ids" type="select" label="Enter your IDs (UniProt Accession number or Gene ID)" help="Copy/paste or from a file (e.g. table)" >
                 <option value="text">Copy/paste your IDs</option>
                 <option value="file" selected="true">Input file containing your IDs</option>
             </param>
@@ -82,8 +82,8 @@
         </conditional>
         <conditional name="idti" >
             <param name="idtypein" type="select" label="Select type/source of IDs" help="" >
-                <option value="Uniprot">UniProt accession number (e.g.:P31946)</option>
-                <option value="Entrez">Entrez Gene ID (e.g.:4151)</option>
+                <option value="Uniprot">UniProt accession number (e.g. P31946)</option>
+                <option value="Entrez">Entrez Gene ID (e.g. 4151)</option>
             </param>
             <when value="Uniprot"/>
             <when value="Entrez"/>
@@ -101,7 +101,7 @@
         <conditional name="ggo">
             <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories representation analysis?"/>
             <when value="true">
-                <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level)">
+                <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level, up to 3)">
 				    <option value="1">1</option>
 				    <option value="2" selected="True">2</option>
 				    <option value="3">3</option>
@@ -143,7 +143,7 @@
                             </when>
                         </conditional>
                         <conditional name="universe_idti" >
-                            <param name="universe_idtypein" type="select" label="Select type of background IDs" help="" >
+                            <param name="universe_idtypein" type="select" label="Select type of IDs of your background" help="" >
                                 <option value="Uniprot">UniProt Accession number</option>
                                 <option value="Entrez">Entrez Gene ID</option>
                             </param>
@@ -238,7 +238,11 @@
 
 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).
 
-"Select type/source of IDs": only entrez gene ID (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE. 
+"Select type/source of IDs": only entrez gene ID (e.g. 4151, 7412) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE. 
+
+.. class:: warningmark
+	
+In copy/paste mode, the number of IDs considered in input is limited to 5000.
 
 -----
 
@@ -272,6 +276,7 @@
 -----
 
 **Authors**
+
 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. 
 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
 
@@ -282,24 +287,25 @@
 
 .. class:: infomark
 
-Packages used: 
+Bioconductor Packages used: 
+
     - bioconductor-org.hs.eg.db v3.5.0
     - bioconductor-org.mm.eg.db v3.5.0
     - bioconductor-org.rn.eg.db v3.5.0
     - dose v3.2.0
-    - clusterpofiler v 3.4.4
+    - clusterprofiler v 3.4.4
 
 .. class:: infomark
 
 **Galaxy integration**
 
-T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+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.
 
 
     ]]></help>