--- a/build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.5.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="develop">
   <description>Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type):
  -f "$type"
@@ -65,6 +65,10 @@
     <data format="tsv" name="outputPath"/>
   </outputs>
   <tests/>
-  <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search. See McSha et al. 2003 (https://doi.org/10.1093/bioinformatics/btg217), Rahman et al. 2005 (https://doi.org/10.1093/bioinformatics/bti116) and Pertusi et al. 2014 (https://doi.org/10.1093/bioinformatics/btu760)]]></help>
-  <citations/>
+  <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search.]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btg217</citation>
+    <citation type="doi">10.1093/bioinformatics/bti116</citation>
+    <citation type="doi">10.1093/bioinformatics/btu760</citation>
+  </citations>
 </tool>