Mercurial > repos > metexplore > met4j_topologicalpathwayanalysis

changeset 3:fcb3f990694e 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 15:33:40 +0000
parents e358eca5d70a
children
files TopologicalPathwayAnalysis.xml macros.xml
diffstat 2 files changed, 3 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/TopologicalPathwayAnalysis.xml	Fri Nov 21 10:24:19 2025 +0000
+++ b/TopologicalPathwayAnalysis.xml	Wed Jan 21 15:33:40 2026 +0000
@@ -39,34 +39,7 @@
   <outputs>
     <data format="tsv" name="outputPath"/>
   </outputs>
-  <tests>
-    <test>
-      <param name="inputPath" value="XF_network.sbml"/>
-      <param name="dataPath" value="XF_network_C_NOI.txt"/>
-      <param name="inputSide" value="XF_network_C_Side.tab"/>
-      <output name="outputPath">
-        <assert_contents>
-          <has_n_columns n="3"/>
-          <has_n_lines n="3"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="inputPath" value="XF_network.sbml"/>
-      <param name="dataPath" value="XF_network_C_NOI.txt"/>
-      <param name="inputSide" value="XF_network_C_Side.tab"/>
-      <param name="undirected" value="true"/>
-      <param name="removeIsolated" value="true"/>
-      <param name="out" value="true"/>
-      <param name="mergingStrat" value="by_id"/>
-      <output name="outputPath">
-        <assert_contents>
-          <has_n_columns n="3"/>
-          <has_n_lines n="3"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
+  <tests/>
   <help><![CDATA[Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds.
 From a list of compounds of interest, the app compute their betweenness centrality (which quantifies how often a compound acts as a intermediary along the shortest paths between pairs of other compounds in the network, which, if high, suggest a critical role in the overall flow within the network). Each pathway is scored according to the summed centrality of its metabolites found in the dataset. Alternatively to the betweenness, one can make use of the out-degree (the number of outgoing link, i.e. number of direct metabolic product) as a criterion of importance. TPA is complementary to statistical enrichment analysis to ensures a more meaningful interpretation of the data, by taking into account the influence of identified compounds on the structure of the pathways.
 @ATTRIBUTION@]]></help>
--- a/macros.xml	Fri Nov 21 10:24:19 2025 +0000
+++ b/macros.xml	Wed Jan 21 15:33:40 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**