# HG changeset patch
# User proteore
# Date 1579767371 18000
# Node ID f53249651adda3b3963537eaeab308ea326daa25
# Parent  a6e33a8ae6ff650e40295232986a21d854904b4f
planemo upload commit c9d70181a2b587e53dcc4b5885b74b625def6b8c-dirty

diff -r a6e33a8ae6ff -r f53249651add GO_terms_enrich_comparison.xml
--- a/GO_terms_enrich_comparison.xml	Tue Jan 14 08:51:51 2020 -0500
+++ b/GO_terms_enrich_comparison.xml	Thu Jan 23 03:16:11 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="go_terms_enrich_comparison" name="GO terms enrich comparison " version="2020.01.14">
+<tool id="go_terms_enrich_comparison" name="GO terms enrich comparison " version="2020.01.23">
     <description>(Human, Mouse, Rat)[clusterProfiler]</description>
     <requirements>
         <requirement type="package">R</requirement>
@@ -38,9 +38,9 @@
         <repeat name="lists" title="List to compare" min="2" max="5" >
 
             <conditional name="input" >
-                <param name="ids" type="select" label="Enter your Gene ID list" help="Copy/paste or from a file (e.g. table)" >
+                <param name="ids" type="select" label="Enter your ID list (Entrez gene ID, e.g. 2810)" 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>
+                    <option value="file" selected="true">Input file containing your list of IDs</option>
                 </param>
                 <when value="text" >
                     <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: 2810 7534' >
@@ -63,7 +63,7 @@
                 </when>
             </conditional>
                 
-            <param name="list_name" type="text" label="name of your list" value="list" optional="false">
+            <param name="list_name" type="text" label="name of your list" value="List" optional="false">
                 <sanitizer>
                     <valid initial="string.printable">
                         <remove value="&apos;"/>
@@ -135,11 +135,9 @@
 
 **Description**
 
-This tool is based on the R package clusterProfiler and allows to compare GO terms enrichment analyses of gene/protein sets. 
+This tool is based on the R package clusterProfiler and was developed for biological theme comparison; it provides a function to automatically calculate enriched functional categories of each gene clusters provided by the user and to compare them. 
 Given a list of gene set, this function will compute GO enrichment profiles of each gene list.
 
-This tool calculates GO categories enrichment (over- or under-representation) for the IDs of the input list. 
-
 -----
 
 **Input**
@@ -149,17 +147,17 @@
 "Enter your Gene ID list": only Entrez Gene ID (e.g : 4151, 7412).  
 If your IDs are not Entrez Gene IDs, please use the ID_Converter tool of ProteoRE. 
 
-"Does file contain header?": in case of file input, you specify if there is header or not. 
+"Does file contain header?": specify if there is header in your input file. 
 
-"Column number of IDs": in which column are your IDs. (e.g. for column 2 you write "c2")
+"Column number of IDs": in which column are your IDs. (e.g. for column 2, type "c2")
 
-"name of your list": write the name for this list
+"name of your list": enter a name for each list ("List" by default); this name will be used in the output files. up to five lists can be considered
 
 -----
 
 **Parameters**
 
-"Species": the three supported species are Homo sapiens, Mus musculus and Rattus norvegicus 
+"Species": the following three species are currently supported: Homo sapiens, Mus musculus and Rattus norvegicus 
 
 "Select GO terms category": allows you to perform analysis on one, two or three categories of the Gene Ontology. The categories are 
 Cellular Component (CC), Biological Process (BP) and Molecular Function (MF). 
@@ -168,10 +166,10 @@
 
 **Output**
 
-Diagram output: graphical output in the form of a dot-plot (png, jpeg or pdf format), one figure for each GO category. 
-Text tables: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) 
+Diagram output: graphical output in the form of a dot-plot (png, jpeg or pdf format), one figure for each GO category. The dots size correspond to the value of the GeneRatio (i.e. gene counts / total number of gene list), the bigger the dot size, the higher the GeneRatio. The dots in the plot are color-coded based on their corresponding (adjusted) p-values. Color gradient ranging from red to blue correspond to in order of increasing p-values. That is, red indicate low p-values (high enrichment), and blue indicate high p-values (low enrichment).
+Text tables with the following information: GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) 
 and GO term frequency (e.g. BP.Frequency). 
-One table and one graphic will be produced for each GO category. 
+One table and one graphic are created for each GO category. 
 
 -----
 
@@ -190,7 +188,7 @@
 
 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
+David Christiany, 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.