# HG changeset patch
# User metexplore
# Date 1769009354 0
# Node ID 04279576894034f4cdfbf584af6e796f3b6840d9
# Parent  27be7e97f255f4f3f3276a922b9c51edb829ad3d
planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170

diff -r 27be7e97f255 -r 042795768940 ExtractSubNetwork.xml
--- a/ExtractSubNetwork.xml	Tue Oct 28 14:20:25 2025 +0000
+++ b/ExtractSubNetwork.xml	Wed Jan 21 15:29:14 2026 +0000
@@ -48,37 +48,29 @@
       <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="format" value="gml"/>
-      <output ftype="txt" name="output">
-        <assert_contents>
-          <has_line_matching expression=".*node.*" n="3"/>
-          <has_line_matching expression=".*edge.*" n="2"/>
-        </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 of interests ids, one per row.
 The subnetwork corresponds to the part of the network that connects compounds from the first list to 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. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting.
 See previous works on subnetwork extraction for parameters recommendations.
 @ATTRIBUTION@]]></help>
   <citations>
+    <citation type="doi">10.1093/nar/gki437</citation>
+    <citation type="doi">10.1093/bioinformatics/btu760</citation>
+    <citation type="doi">10.1093/bib/bbv115</citation>
+    <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
+    <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
+    <citation type="doi">10.1093/nar/gki437</citation>
+    <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
+    <citation type="doi">10.1093/bioinformatics/btg217</citation>
     <citation type="doi">10.1093/bib/bbv115</citation>
     <citation type="doi">10.1093/bioinformatics/bti116</citation>
-    <citation type="doi">10.1093/nar/gki437</citation>
-    <citation type="doi">10.1093/bioinformatics/btg217</citation>
-    <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
     <citation type="doi">10.1093/bioinformatics/btu760</citation>
-    <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
   </citations>
 </tool>
diff -r 27be7e97f255 -r 042795768940 macros.xml
--- a/macros.xml	Tue Oct 28 14:20:25 2025 +0000
+++ b/macros.xml	Wed Jan 21 15:29:14 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**