Mercurial > repos > metexplore > met4j_extractsubbipnetwork

changeset 3:dc9011ea45f6 draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
author metexplore
date Wed, 21 Jan 2026 15:29:07 +0000
parents e362dda04176
children
files ExtractSubBipNetwork.xml macros.xml
diffstat 2 files changed, 4 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- 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.
--- 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**