--- a/reactome_analysis.xml	Mon Nov 26 04:48:25 2018 -0500
+++ b/reactome_analysis.xml	Fri Dec 07 10:43:57 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="reactome_analysis" name="Reactome" version="2018.10.12">
+<tool id="reactome_analysis" name="Reactome" version="2018.12.07">
     <description>display your protein list on the Reactome pathway browser</description>
     <requirements>
     </requirements>
@@ -6,11 +6,16 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
+
+        python $__tool_directory__/reactome_analysis.py 
         #if $opt.input == "text"
-            python $__tool_directory__/reactome_analysis.py --json "$opt.list" "list" --output "$output" --trash "$trash"
+        --json "$opt.list" "list" 
         #else if $opt.input == "file"
-            python $__tool_directory__/reactome_analysis.py --json "$opt.file" "file" $opt.header $opt.ncol --output "$output" --trash "$trash"
+        --json "$opt.file" "file" "$opt.header" "$opt.ncol" 
         #end if
+        --output "$output" 
+        --trash "$trash"
+        --species "$species"
         
     ]]></command>
     <inputs>
@@ -36,8 +41,12 @@
                 <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 number where are your IDs (e.g : Enter c1 for column n°1)" />
             </when>
-            
         </conditional>
+        <param name="species" type="select" label="Select species">
+            <option value="48887">Human (H. sapiens)</option>
+            <option value="48892">Mouse (M. musculus)</option>
+            <option value="48895">Rat (R. norvegicus)</option>
+        </param>
     </inputs>
     <outputs>
         <data name="output" format="html" label="" />
@@ -64,6 +73,8 @@
 
 **Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7). If there is any ID containing invalid characters, it will be removed from the queue and placed in "Invalid identifiers" file.**
 
+**Supported species: Human (H. sapiens), Mouse (M. musculus), Rat (Rattus norvegicus)**
+
 -----
 
 .. class:: infomark