--- a/tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml	Thu Nov 17 07:57:52 2022 +0000
+++ b/tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml	Thu Jan 12 13:45:13 2023 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.2.0">
+<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.2.1">
   <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:1.2.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type):
  -f "$type"
@@ -50,7 +50,7 @@
     </param>
     <param argument="-d" checked="false" falsevalue="" label="Use distance rather than similarity" name="dist" truevalue="-d" type="boolean" value="false"/>
     <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
-    <param argument="-sc" format="" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
+    <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
     <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
       <option selected="true" value="no">no</option>
       <option value="by_name">by_name</option>
@@ -62,7 +62,7 @@
     <param argument="-nan" checked="false" falsevalue="" label="do not output edges with undefined weight" name="removeNaN" truevalue="-nan" type="boolean" value="false"/>
   </inputs>
   <outputs>
-    <data format="" name="outputPath"/>
+    <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>