--- a/Sbml2CompoundGraph.xml	Fri Nov 21 10:22:24 2025 +0000
+++ b/Sbml2CompoundGraph.xml	Wed Jan 21 15:31:36 2026 +0000
@@ -46,40 +46,13 @@
       <option value="nodeList">nodeList</option>
       <option value="json">json</option>
       <option value="matrix">matrix</option>
+      <option value="jsonviz">jsonviz</option>
     </param>
   </inputs>
   <outputs>
     <data format="txt" name="output"/>
   </outputs>
-  <tests>
-    <test>
-      <param name="inputPath" value="XF_network.sbml"/>
-      <param name="inputSide" value="XF_network_C_Side.tab"/>
-      <param name="format" value="gml"/>
-      <output name="output">
-        <assert_contents>
-          <has_line_matching expression=".*node.*" n="1101"/>
-          <has_line_matching expression=".*edge.*" n="5581"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="inputPath" value="XF_network.sbml"/>
-      <param name="inputSide" value="XF_network_C_Side.tab"/>
-      <param name="undirected" value="true"/>
-      <param name="computeWeight" value="true"/>
-      <param name="removeIsolated" value="true"/>
-      <param name="degree" value="true"/>
-      <param name="mergingStrat" value="by_id"/>
-      <param name="format" value="gml"/>
-      <output name="output">
-        <assert_contents>
-          <has_line_matching expression=".*node.*" n="793"/>
-          <has_line_matching expression=".*edge.*" n="9372"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
+  <tests/>
   <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes.
 While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations.
 In contrary to the Sbml2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.