# HG changeset patch
# User proteore
# Date 1542879474 18000
# Node ID 682041ae727d1c98a6eccbd065f209f256525598
# Parent  da82872f5c80adb17f3998031a5127ed248ffc3e
planemo upload commit 170560760f17fd1b77efe8bb95fedf3eb2433f0b-dirty

diff -r da82872f5c80 -r 682041ae727d kegg_pathways_visualization.xml
--- a/kegg_pathways_visualization.xml	Mon Nov 12 10:54:25 2018 -0500
+++ b/kegg_pathways_visualization.xml	Thu Nov 22 04:37:54 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.12">
+<tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.22">
     <description>map visualisation (PathView)</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
@@ -146,12 +146,12 @@
             </when>
         </conditional>
         <param name="id_type" type="select" label="Select your identifiers type :">
+            <option value="geneID" selected="true">Entrez gene ID</option>
+            <option value="keggid">KEGG genes ID</option>
             <option value="uniprotID">Uniprot Accession number</option>
-            <option value="geneID">Entrez gene ID</option>
-            <option value="keggid">KEGG genes ID</option>
         </param>
         <conditional name="input" >
-            <param name="ids" type="select" label="Enter your identifiers (Uniprot AC or Entrez gene ID)" help="Copy/paste or ID list from a file (e.g. table)" >
+            <param name="ids" type="select" label="Enter your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
                 <option value="text">Copy/paste your identifiers</option>
                 <option value="file" selected="true">Input file containing your identifiers</option>
             </param>
@@ -225,9 +225,9 @@
         </test-->
     </tests>
     <help><![CDATA[
-This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
+This tool map a list identifiers to KEGG pathway with the R package 'pathview'.
 
-You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat.
+You can map Entrez gene ID, KEGG genes ID or Uniprot accession number from three species : human, mouse and rat.
 
 If your input have another type of IDs, please use the ID_Converter tool.
 
@@ -238,8 +238,8 @@
     - chosing from the KEGG pathways name list 
     - giving a list (copy/paste)
     - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column)
-- Genes/proteins ids to map can be either a list of Entrez genes IDs / Uniprot accession number or a file (tabular, tsv, txt) containing at least one column of Entrez genes IDs / Uniprot accession number. 
-- fold change values (up to three columns) from a dataset (same dataset as for Genes/proteins ids to map)
+- Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number or in a column of a file (tabular, tsv, txt). 
+- Fold change values (up to three columns) from a dataset (same dataset as identifiers to map) can be added.
 
 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values.