# HG changeset patch
# User metexplore
# Date 1769009496 0
# Node ID e4862cbda53adec1cf2c15f7a304f1580b2c36e6
# Parent  c6d7b50aa5b920278499727be9ff9b7ac1e41563
planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170

diff -r c6d7b50aa5b9 -r e4862cbda53a Sbml2CompoundGraph.xml
--- 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.
diff -r c6d7b50aa5b9 -r e4862cbda53a macros.xml
--- a/macros.xml	Fri Nov 21 10:22:24 2025 +0000
+++ b/macros.xml	Wed Jan 21 15:31:36 2026 +0000
@@ -3,7 +3,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.2.0">met4j</requirement>
+            <requirement type="package" version="2.2.1">met4j</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -12,7 +12,7 @@
             <xref type="bio.tools">met4j</xref>
         </xrefs>
     </xml>
-    <token name="@TOOL_VERSION@">2.2.0</token>
+    <token name="@TOOL_VERSION@">2.2.1</token>
     <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**