--- a/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="0.11.0">
+<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="0.12.0">
   <description>Scan a network to identify side-compounds.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath"
  $sideOnly
@@ -80,4 +80,5 @@
 Being tightly coupled to another compound through a high number of redundant edges, can point out cofactors while keeping converging pathways' products with high degree like pyruvate aside.  
 - *Carbon Count*: Metabolic "waste", or degradation end-product such as ammonia or carbon dioxide are usually considered as side compounds.
 Most of them are inorganic compound, another ill-defined concept, sometimes defined as compound lacking C-C or C-H bonds. Since chemical structure is rarely available in SBML model beyond chemical formula, we use a less restrictive criterion by flagging compound with one or no carbons. This cover most inorganic compounds, but include few compounds such as methane usually considered as organic.  - *Chemical Formula*: Metabolic network often contains 'artifacts' that serve modelling purpose (to define a composite objective function for example). Such entities can be considered as 'side entities'. Since they are not actual chemical compounds, they can be detected by their lack of valid chemical formula. However, this can also flag main compounds with erroneous or missing annotation.]]></help>
+  <citations/>
 </tool>