--- a/rp2biosensor.xml	Wed Jan 05 16:14:32 2022 +0000
+++ b/rp2biosensor.xml	Fri Feb 25 07:16:18 2022 +0000
@@ -1,24 +1,36 @@
-<tool id="rp2biosensor" name="rp2biosensor" version="1.0.1">
+<tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@" profile="19.09">
     <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.1.0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.0.1">rp2biosensor</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python -m rp2biosensor
         '$rp2_results'
         --opath '$html_file'
+        #if str($adv.json_graph) == "true"
+            --ojson '$json_file'
+        #end if
     ]]></command>
     <inputs>
         <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/>
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
+        </section>
     </inputs>
     <outputs>
         <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/>
+        <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}">
+            <filter> adv['json_graph'] </filter>
+        </data>
     </outputs>
     <tests>
         <test>
         <!-- test 1: check if identical outputs are produced -->
-        <param name="rp2_results" value="rp2-results_dmax-16.csv" />
-        <output name="html_file" md5="4abb29e769106e75e68a939764dd2e31"/>
+        <param name="rp2_results" value="rp2-results-lactate.csv" />
+        <output name="html_file" md5="88ba7cd2501c4d671b9eac396e7b4af9"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -39,7 +51,9 @@
 
 * **opath**\ : (string) Output path. Default: biosensor.html.
 
-* **o_sbol_dir**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file.
+* **otype**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file.
+
+* **ojson**\ : (string) Output the graph as json file if the path is not None. Default: None
 
 Project Links
 ------------------
@@ -49,7 +63,7 @@
 Version
 ----------
 
-1.0.1
+2.1.0
 
 Authors
 -------