--- a/reactome_analysis.xml	Sun Nov 26 19:29:17 2017 -0500
+++ b/reactome_analysis.xml	Fri Feb 16 03:43:58 2018 -0500
@@ -16,19 +16,15 @@
     ]]></command>
     <inputs>
         <conditional name="opt">
-            <param name="input" type="select" label="Input identifiers" multiple="False" >
+            <param name="input" type="select" label="Input identifiers (Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157) or gene name (e.g. AQP7)" multiple="False" >
                 <option value="text">Copy/paste your list of IDs </option>
-                <!--option value="file">Choose a single-column file </option-->
-		        <option value="file">Choose a multiple-columns file </option>
+		        <option value="file">Input file containing your identifiers</option>
             </param>
             <when value="text" >
                 <param name="list" type="text" label="Enter list of identifiers" />
             </when>
-            <!--when value="file" >
-                <param name="idfile" type="data" format="txt" label="Choose a single-column file" />
-            </when-->
             <when value="file" >
-                <param name="file" type="data" format="txt, tabular" label="Choose a multiple-columns file" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" />
+                <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" />
                 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
 		        <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' />
             </when>
@@ -42,21 +38,40 @@
     <tests>
         <test>
             <conditional name="opt" >
-                <param name="input" value="mq" />
-                <param name="file" value="UnipIDs.txt" />
-                <param name="header" value="false" />
+                <param name="input" value="file" />
+                <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
+                <param name="header" value="true" />
                 <param name="ncol" value="c1" />
             </conditional>
-            <output name="output" file="reactome_output.html" ftype="html" />
-            <output name="trash" file="reactome_invalide_ids.txt" ftype="tab" />
+            <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" />
+            <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" />
         </test>
     </tests>
     <help><![CDATA[
 Reactome software provides service of creating diagram representing the relations between the biological processes. This tool allows linking to Reactome web service with pre-loaded data from a list of IDs, a file containing IDs or from a column of a complexed file.
 
 **For the rows that have more than 1 ID, only the first one is taken into account**
+**Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7)**
 
-**This tool only accepts letters (a-z or A-Z), numbers (0-9) and 3 characters "." "-" "_" for IDs. If there is ID containing other than these characters, it will be removed from the queue and placed in "Invalid identifiers" file**
+-----
+
+.. class:: infomark
+
+**Authors** 
+
+Fabregat et al. 2017 PMID: 29145629 (https://www.ncbi.nlm.nih.gov/pubmed/29145629)
+
+Milacic et al. 2012 PMID:24213504 (https://www.ncbi.nlm.nih.gov/pubmed/24243840)
+
+.. class:: infomark
+
+**Galaxy integration**
+
+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,
+
+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
     ]]></help>
     <citations>
     </citations>