# HG changeset patch
# User proteore
# Date 1596183519 0
# Node ID 3c5813b29486879015eed7e154f70479033279eb
# Parent  381e18f13ed2dd2f7a91ddd97da15fa558a65d2f
"planemo upload commit b218f949aa7a17b1e75a35946a3a19194bf168f3-dirty"

diff -r 381e18f13ed2 -r 3c5813b29486 add_protein_features.xml
--- a/add_protein_features.xml	Thu Jul 30 09:45:47 2020 +0000
+++ b/add_protein_features.xml	Fri Jul 31 08:18:39 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="prot_features" name="Add protein features" version="2020.07.30.1">
+<tool id="prot_features" name="Add protein features" version="2020.07.31">
 <description>[neXtProt, Human]
 </description>
 <requirements>
@@ -66,19 +66,19 @@
         <option value="Uniprot_AC" selected="false">UniProt accession number</option>
     </param>
     <param name="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="false">
-        <option value="SeqLength" selected="false">Sequence Length</option>
+        <option value="ProteinName" selected="false">Protein name</option>
+	    <option value="SeqLength" selected="false">Sequence Length</option>
         <option value="MW" selected="false">Molecular Weight</option>
         <option value="IsoPoint" selected="false">Isoelectric point</option>
         <option value="TMDomains" selected="false">Number of transmembrane domains</option>
-        <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option>
-        <option value="Chr" selected="false">Chromosome</option>
-        <option value="SubcellLocations" selected="false">Subcellular Location</option>
+       	<option value="SubcellLocations" selected="false">Subcellular Location</option>
         <option value="Diseases" selected="false">Disease information</option>
-        <option value="ProteinName" selected="false">Protein name</option>
         <option value="Function" selected="false">Protein function</option>
         <option value="PostTranslationalModifications" selected="false">Post translational modifications</option>
         <option value="ProteinFamily" selected="false">Protein family</option>
         <option value="Pathway" selected="false">Pathway(s)</option>
+	    <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option>
+        <option value="Chr" selected="false">Chromosome</option>
     </param>
 
     <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
@@ -118,7 +118,7 @@
 
 **Description**
 
-This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich your protein IDs list.
+This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich and better inform your protein IDs list.
 
 -----
 
@@ -140,7 +140,7 @@
 
 **Output**
 
-Output is a tabular file containing both original columns and new columns including the annotation requested.  
+Output is a tabular file containing both original columns and new columns including the annotation requested. Only features/annotations assigned with a "GOLD" quality criterion are considered, otherwise a "NA" value is returned.
 
 .. class:: warningmark
 
@@ -154,8 +154,9 @@
 
  neXtProt releases : 
  
-- nextProt release 07-05-2019 (release Feb 13, 2019)
-- neXtProt release 08-10-2018 (release Feb 21, 2018)
+- nextProt release 31-07-2020 (release Feb, 2020)
+- nextProt release 07-05-2019 (release Feb, 2019)
+- neXtProt release 08-10-2018 (release Feb, 2018)
   
 .. class:: warningmark
 
@@ -167,7 +168,7 @@
 
 **Authors**
 
-David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+David Christiany, Lisa Perus, T.P. 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