# HG changeset patch
# User proteore
# Date 1561623635 14400
# Node ID 005221a20848d20c606138c2c7fe81be25c1edac
# Parent  f4e02d20546b4001705ea68edc43e0fcf836abf2
planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty

diff -r f4e02d20546b -r 005221a20848 kegg_maps_visualization.xml
--- a/kegg_maps_visualization.xml	Tue May 14 09:28:50 2019 -0400
+++ b/kegg_maps_visualization.xml	Thu Jun 27 04:20:35 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.05.14">
+<tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.06.27">
     <description>of (differentially expressed) genes/proteins [KEGG]</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
@@ -38,7 +38,7 @@
     ]]></command>
     <inputs>
         <!--section name="pathways_section" title="Pathways" expanded="True"--> 
-            <conditional name="species">
+            <conditional name="species (human, mouse, rat)">
                 <param name="ref_file" type="select" label="Species" >
                     <option value="hsa">Human (Homo sapiens)</option>
                     <option value="mmu">Mouse (Mus musculus)</option>
@@ -200,7 +200,7 @@
         <!--/section-->
         <param name="native" type="select" label="Graphical format">
             <option value="true">KEGG map (.png)</option>
-            <option value="false">Graphviz layout engine (.pdf)</option> 
+            <option value="false">KEGG map, graphviz layout engine (.pdf)</option> 
         </param>
     </inputs>
     <outputs>
@@ -246,7 +246,7 @@
 
 **Description**
 
-This tool based on the Pathview R package, is set for pathway based data integration and visualization. 
+This tool, relying on the Pathview R package, is set for pathway based data integration and visualization. 
 
 It maps and renders a wide variety of biological data on relevant KEGG pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data.
 
@@ -277,24 +277,24 @@
 If there's more than one ID per line in the specified column, it will be splitted resulting in one unique ID per line. For example this table:
 
 .. csv-table:: Simulated data
-   :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
+   :header: "Entrez_gene_ID","UniProt.AC","UniProt.ID"
 
-    "ENSG00000136881","Q14032","BAAT_HUMAN"
-    "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
-    "ENSG00000244731","P0C0L4","CO4A_HUMAN"
+    "6881","Q14032","BAAT_HUMAN"
+    "70099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
+    "731","P0C0L4","CO4A_HUMAN"
 
 |
 
 will be converted as follow:
 
 .. csv-table:: Simulated data
-   :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
+   :header: "Entrez_gene_ID","UniProt.AC","UniProt.ID"
 
-    "ENSG00000136881","Q14032","BAAT_HUMAN"
-    "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
-    "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
-    "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
-    "ENSG00000244731","P0C0L4","CO4A_HUMAN"
+    "6881","Q14032","BAAT_HUMAN"
+    "70099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
+    "70099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
+    "70099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
+    "731","P0C0L4","CO4A_HUMAN"
 
 |
 
@@ -302,7 +302,7 @@
 
 **Output:**
 
-- a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway.
+- a set of graphical map, i.e. a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each KEGG map.
 
 - a **summary text file** (.tsv) of the mapping(s) with the following columns
     - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
@@ -345,7 +345,7 @@
 
 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>
     <citations>
         <citation type="doi">10.1093/nar/gkx372</citation>