--- a/add_protein_features.xml	Thu Dec 13 03:57:57 2018 -0500
+++ b/add_protein_features.xml	Mon Mar 11 04:39:31 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="prot_features" name="Add protein features" version="2018.12.12">
+<tool id="prot_features" name="Add protein features" version="2019.03.10">
 <description>[neXtProt]
 </description>
 <requirements>
@@ -23,18 +23,23 @@
   --localization='$Nextprot_params.localization' 
   --diseases_info='$Nextprot_params.diseases_info'  
   --output='$output'  
-  --nextprot=$__tool_directory__/tool-data/result_nextprot.txt 
+
+  #if 'nextprot_ref' in str($ref_file).split("/")
+    --nextprot="$ref_file" 
+  #else 
+    --nextprot="$__tool_directory__/$ref_file"
+  #end if 
     
 ]]></command>
 
 <inputs>
   <conditional name="inputtype">
-    <param name="filetype" type="select" label="Select your type of input file"> 
-      <option value="file" selected="true">Input file containing your identifiers (neXtProt or Uniprot ID)</option>
+    <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt)" help="Copy/paste or from a file" > 
+      <option value="file" selected="true">Input file containing your IDs </option>
       <option value="copy_paste">Copy/paste your list of IDs</option> 
     </param>
     <when value="copy_paste">
-      <param name="genelist" type="text" label="Enter a list of identifiers separated by tab, space or carriage return into the form field" help="for example : A0AVI2 A6NGB0">
+      <param name="genelist" type="text" label="Enter a list of IDs separated by tab, space or carriage return into the form field" help="for example : A0AVI2 A6NGB0">
         <sanitizer invalid_char="">
             <valid initial="string.printable">
                 <remove value="&apos;"/>
@@ -50,19 +55,20 @@
       </param>
     </when>
     <when value="file">
-      <param name="genelist" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="This file must imperatively have 1 column filled with IDs consistent with the neXtprot database (Uniprot accession number or neXtProt ID). If this is not the case, please use the ID_Converter tool."/>
-      <param name="column" type="text" label="Please specify the column where are your IDs (e.g : Enter c1 for column n°1)" value="c1"/> 
-      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file have a header?" />
-
+      <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
+      <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1">
+        <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+      </param>
+      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />
     </when>
   </conditional>
 
-      <param name="idtype" type="select" label="Type of your input ids" multiple="false" optional="false"> 
+      <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> 
  		      <option value="Uniprot_AC" selected="true">Uniprot accession number</option>
           <option value="NextprotID" selected="false">neXtProt IDs</option>
       </param>
-      <section name="Nextprot_params" title="Select features of interest (compulsory step)" expanded="True">
-        <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="Choose the information you want to add to your data from Nextprot" display="checkboxes" optional="true"> 
+      <section name="Nextprot_params" title="Select features" expanded="True">
+        <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="false"> 
           <option value="SeqLength" selected="false">Sequence Length</option>
           <option value="MW" selected="false">Molecular Weight</option>
           <option value="IsoPoint" selected="false">Isoelectric point</option>
@@ -70,14 +76,17 @@
           <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option>
         </param>
 
-        <param name="localization" type="select" label="Localization" multiple="true" help="Choose the information you want to add to your data from Nextprot" display="checkboxes" optional="true"> 
+        <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true"> 
  		      <option value="Chr" selected="false">Chromosome</option>
  		      <option value="SubcellLocations" selected="false">Subcellular Location</option>
         </param>
 
-        <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Diseases informations" />
+        <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" />
 
       </section>
+      <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
+        <options from_data_table="proteore_nextprot_ref"/>
+      </param>
 
 </inputs>
 
@@ -112,22 +121,36 @@
 
 <help><![CDATA[
 
-This tool add annotation (protein features) from neXtProt database (knowledge base on human proteins) to your protein IDs list.
+**Description**
+
+This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich your protein IDs list.
+
+-----
 
 **Input**
 
-Input can be a file containing multiple fields but with **at least one column of Uniprot accession number or neXtProt IDs**. If your input file contains other type of IDs, please use the ID_Converter tool.  
+A list of of Uniprot Accession Number (e.g. P05090) or neXtProt IDs (e.g. NX_P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number or neXtProt IDs**. If your input file contains other type of IDs, please use the ID_Converter tool.  
+
+-----
+
+**Parameters**
+
+"Select features": three categories of annotation can be retrieved: physico-chemical features, localisation (chromosome, subcellular) and disease information (set to "Yes" by default). Select each feature according to your interest by clicking the corresponding checkbox. 
+
+-----
 
-**Databases**
+**Output**
+
+Output is a tabular file containing both original columns and new columns including the annotation requested.  
 
-Annotations have been retrieved from the neXtProt released on 21/02/2018 using the latest data from peptideAtlas (release Human 2018-1)
+-----
+
+**Data source (release date)**
+
+Annotations have been retrieved from the neXtProt released on 21/02/2018 using the latest data from peptideAtlas (release January 2018)
 
 using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et  al., 2017)
 
-**Outputs**
-
-The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected.  
-
 -----
 
 .. class:: infomark
@@ -136,7 +159,7 @@
 
 David Christiany, Lisa Peru, 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
+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.