# HG changeset patch
# User metexplore
# Date 1769009347 0
# Node ID dc9011ea45f618db92ee8006f78597f9d49982cb
# Parent  e362dda0417668b8a1bc76fd55304e75b1debc0d
planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170

diff -r e362dda04176 -r dc9011ea45f6 ExtractSubBipNetwork.xml
--- a/ExtractSubBipNetwork.xml	Tue Oct 28 14:20:19 2025 +0000
+++ b/ExtractSubBipNetwork.xml	Wed Jan 21 15:29:07 2026 +0000
@@ -46,26 +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="toy_model.xml"/>
-      <param name="sourcePath" value="seeds.txt"/>
-      <param name="targetPath" value="targets.txt"/>
-      <param name="sideCompoundFile" value="sc.txt"/>
-      <param name="format" value="gml"/>
-      <output ftype="txt" name="output">
-        <assert_contents>
-          <has_line_matching expression=".*node.*" n="5"/>
-          <has_line_matching expression=".*edge.*" n="4"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
+  <tests/>
   <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
 The subnetwork corresponds to the part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list.
 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.
diff -r e362dda04176 -r dc9011ea45f6 macros.xml
--- a/macros.xml	Tue Oct 28 14:20:19 2025 +0000
+++ b/macros.xml	Wed Jan 21 15:29:07 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**