# HG changeset patch
# User metexplore
# Date 1656337268 0
# Node ID 9b162ee6ff8ed4a6cb23dc2267cf28614f8e0ada
# Parent  dcd16521b9692d169293600d1b18cec7872928b8
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95

diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/ExtractPathways/ExtractPathways.xml
--- a/tools/attributes/ExtractPathways/ExtractPathways.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/ExtractPathways/ExtractPathways.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractPathways" name="ExtractPathways" version="0.11.0">
+<tool id="met4j_ExtractPathways" name="ExtractPathways" version="0.12.0">
   <description>Extract pathway(s) from GSMN</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 attributes.ExtractPathways -i "$inputPath"
  -p "$pathwayId"
@@ -36,4 +36,5 @@
     </test>
   </tests>
   <help><![CDATA["Extract pathway(s) from GSMN: From a SBML file, Create a sub-network SBML file including only a selection of pathways]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml
--- a/tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="0.11.0">
+<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="0.12.0">
   <description>Extract databases' references from SBML annotations or notes.</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 attributes.ExtractSbmlAnnot -i "$inputPath"
  -export "$export"
@@ -71,4 +71,5 @@
     </test>
   </tests>
   <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml
--- a/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="0.11.0">
+<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="0.12.0">
   <description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</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 attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan':
  -cc "$colcharge"
@@ -115,4 +115,5 @@
 The charge will be written in the SBML file in two locations:+
 - in the reaction notes (e.g. <p>charge: -1</p>)
 - as fbc attribute (e.g. fbc:charge="1")]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml
--- a/tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.11.0">
+<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.12.0">
   <description>Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC</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 attributes.SbmlSetEcsFromFile#if str($colec) != 'nan':
  -cec "$colec"
@@ -66,7 +66,8 @@
   <help><![CDATA[Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC
 The ids must correspond between the tabulated file and the SBML file.
 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
-The EC will be written in the SBML file in two locations:+
+The EC will be written in the SBML file in two locations:
 - in the reaction notes (e.g. <p>EC_NUMBER: 2.4.2.14</p>)
 - as a reaction annotation (e.g. <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/>)]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml
--- a/tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="0.11.0">
+<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="0.12.0">
   <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</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 attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan':
  -cf "$colformula"
@@ -72,4 +72,5 @@
 - in the metabolite notes (e.g. <p>formula: C16H29O2</p>
 
 - as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml
--- a/tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.11.0">
+<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.12.0">
   <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</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 attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan':
  -cgpr "$colgpr"
@@ -72,11 +72,12 @@
 GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307
 (The GPR will be written in the SBML file in two locations:
 - in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p>
-- as fbc gene product association :       <fbc:geneProductAssociation>
-          <fbc:or>
-            <fbc:geneProductRef fbc:geneProduct="XC_3282"/>
-            <fbc:geneProductRef fbc:geneProduct="XC_0401"/>
-          </fbc:or>
-        </fbc:geneProductAssociation>
+- as fbc gene product association :<fbc:geneProductAssociation>
+ <fbc:or>
+  <fbc:geneProductRef fbc:geneProduct="XC_3282"/>
+  <fbc:geneProductRef fbc:geneProduct="XC_0401"/>
+ </fbc:or>
+</fbc:geneProductAssociation>
 ]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml
--- a/tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="0.11.0">
+<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="0.12.0">
   <description>Set names to network objects from a tabulated file containing the object ids and the names</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 attributes.SbmlSetNamesFromFile#if str($colname) != 'nan':
  -cname "$colname"
@@ -113,4 +113,5 @@
 The ids must correspond between the tabulated file and the SBML file.
 If prefix or suffix is different in the SBML file, use the -p or the -s options.
 ]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml
--- a/tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.11.0">
+<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.12.0">
   <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</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 attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan':
  -cp "$colp"
@@ -87,10 +87,11 @@
 The ids must correspond between the tabulated file and the SBML file.
 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
 Pathways will be written in the SBML file in two ways:- as reaction note (e.g. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group:
-      <groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis">
-        <groups:listOfMembers>
-          <groups:member groups:idRef="R_GLUPRT"/>
-          <groups:member groups:idRef="R_RNDR1b"/>
+<groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis">
+ <groups:listOfMembers>
+  <groups:member groups:idRef="R_GLUPRT"/>
+  <groups:member groups:idRef="R_RNDR1b"/>
 ...
 ]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml
--- a/tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="0.11.0">
+<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="0.12.0">
   <description>Add refs to network objects from a tabulated file containing the metabolite ids and the formulas</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 attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan':
  -cr "$colRef"
@@ -84,4 +84,5 @@
   <help><![CDATA[Add refs to network objects from a tabulated file containing the metabolite ids and the formulas
 Reference name given as parameter (-ref) must correspond to an existing id the registry of  identifiers.org (https://registry.identifiers.org/registry)
 The corresponding key:value pair will be written as metabolite or reaction annotation]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml
--- a/tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="0.11.0">
+<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="0.12.0">
   <description>Create a tabulated file with metabolite attributes from a SBML file</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 attributes.SbmlToMetaboliteTable -s "$sbml"
  -o "$outputFile"
@@ -30,4 +30,5 @@
     </test>
   </tests>
   <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/bigg/GetModelProteome/GetModelProteome.xml
--- a/tools/bigg/GetModelProteome/GetModelProteome.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/bigg/GetModelProteome/GetModelProteome.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_GetModelProteome" name="GetModelProteome" version="0.11.0">
+<tool id="met4j_GetModelProteome" name="GetModelProteome" version="0.12.0">
   <description>Get proteome in fasta format of a model present in BIGG</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 bigg.GetModelProteome -m "$modelId"
  -o "$outputFile"
@@ -31,4 +31,5 @@
     </test>
   </tests>
   <help><![CDATA[Get proteome in fasta format of a model present in BIGG]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/convert/FbcToNotes/FbcToNotes.xml
--- a/tools/convert/FbcToNotes/FbcToNotes.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/convert/FbcToNotes/FbcToNotes.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_FbcToNotes" name="FbcToNotes" version="0.11.0">
+<tool id="met4j_FbcToNotes" name="FbcToNotes" version="0.12.0">
   <description>Convert FBC package annotations to sbml notes</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 convert.FbcToNotes -i "$inputPath"
  -o "$outputPath"
@@ -28,4 +28,5 @@
     </test>
   </tests>
   <help><![CDATA[Convert FBC package annotations to sbml notes]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/convert/Kegg2Sbml/Kegg2Sbml.xml
--- a/tools/convert/Kegg2Sbml/Kegg2Sbml.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/convert/Kegg2Sbml/Kegg2Sbml.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="0.11.0">
+<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="0.12.0">
   <description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</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 convert.Kegg2Sbml#if str($org):
  -org "$org"
@@ -22,17 +22,8 @@
   <outputs>
     <data format="sbml" name="sbml"/>
   </outputs>
-  <tests>
-    <!-- <test maxseconds="600">
-      <param name="org" value="buc"/>
-      <output ftype="sbml" name="sbml">
-        <assert_contents>
-          <is_valid_xml/>
-
-        </assert_contents>
-      </output>
-    </test> -->
-  </tests>
+  <tests/>
   <help><![CDATA[Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.
 Errors returned by this program could be due to Kegg API dysfunctions or limitations. Try later if this problem occurs.]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/convert/Kegg2Sbml/test-data/toy_model.xml
--- a/tools/convert/Kegg2Sbml/test-data/toy_model.xml	Fri Jun 10 10:31:34 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,119 +0,0 @@
-<?xml version="1.0" encoding='UTF-8' ?>
-<sbml fbc:required="false" groups:required="false" level="3" version="1"
-	xmlns="http://www.sbml.org/sbml/level3/version1/core"
-	xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"
-	xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1">
-	<model fbc:strict="true" name="toy model">
-		<listOfUnitDefinitions>
-			<unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
-				<listOfUnits>
-					<unit exponent="-1" kind="gram" multiplier="1" scale="0"/>
-					<unit exponent="1" kind="mole" multiplier="1" scale="-3"/>
-					<unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/>
-				</listOfUnits>
-			</unitDefinition>
-		</listOfUnitDefinitions>
-		<listOfCompartments>
-			<compartment constant="false" id="c" name="Cytosol"/>
-			<compartment constant="false" id="e" name="Extracellular"/>
-		</listOfCompartments>
-		<listOfSpecies>
-			<species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext">
-				<notes>
-					<body xmlns="http://www.w3.org/1999/xhtml">
-						<p>SMILES: C[C@@H](C(=O)O)NC</p>
-					</body>
-				</notes>
-				<annotation>
-					<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-						xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-						<rdf:Description rdf:about="#A_ext">
-							<bqbiol:is>
-								<in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi>
-							</bqbiol:is>
-						</rdf:Description>
-					</rdf:RDF>
-				</annotation>
-
-			</species>
-			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/>
-			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/>
-			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/>
-			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/>
-			<species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/>
-			<species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/>
-			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/>
-		</listOfSpecies>
-		<listOfParameters>
-			<parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/>
-			<parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/>
-			<parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/>
-			<parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/>
-			<parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/>
-			<parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
-			<parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
-			<parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
-			<parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
-			<parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
-		</listOfParameters>
-		<listOfReactions>
-			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false">
-				<listOfReactants>
-					<speciesReference constant="true" species="A_ext" stoichiometry="1.0"/>
-				</listOfReactants>
-				<listOfProducts>
-					<speciesReference constant="true" species="A" stoichiometry="1.0"/>
-				</listOfProducts>
-			</reaction>
-			<reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true">
-				<listOfReactants>
-					<speciesReference constant="true" species="A" stoichiometry="1.0"/>
-				</listOfReactants>
-				<listOfProducts>
-					<speciesReference constant="true" species="B" stoichiometry="1.0"/>
-				</listOfProducts>
-			</reaction>
-			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false">
-				<listOfReactants>
-					<speciesReference constant="true" species="A" stoichiometry="1.0"/>
-				</listOfReactants>
-				<listOfProducts>
-					<speciesReference constant="true" species="C" stoichiometry="1.0"/>
-				</listOfProducts>
-			</reaction>
-			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false">
-				<listOfReactants>
-					<speciesReference constant="true" species="B" stoichiometry="1.0"/>
-					<speciesReference constant="true" species="C" stoichiometry="1.0"/>
-				</listOfReactants>
-				<listOfProducts>
-					<speciesReference constant="true" species="D" stoichiometry="1.5"/>
-				</listOfProducts>
-			</reaction>
-			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false">
-				<listOfReactants>
-					<speciesReference constant="true" species="D" stoichiometry="1.0"/>
-				</listOfReactants>
-				<listOfProducts>
-					<speciesReference constant="true" species="D_ext" stoichiometry="1.0"/>
-				</listOfProducts>
-			</reaction>
-			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false">
-				<listOfReactants>
-					<speciesReference constant="true" species="E_ext" stoichiometry="1.0"/>
-				</listOfReactants>
-				<listOfProducts>
-					<speciesReference constant="true" species="E" stoichiometry="1.0"/>
-				</listOfProducts>
-			</reaction>
-			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false">
-				<listOfReactants>
-					<speciesReference constant="true" species="E" stoichiometry="2.0"/>
-				</listOfReactants>
-				<listOfProducts>
-					<speciesReference constant="true" species="D" stoichiometry="1.0"/>
-				</listOfProducts>
-			</reaction>
-		</listOfReactions>
-	</model>
-</sbml>
\ No newline at end of file
diff -r dcd16521b969 -r 9b162ee6ff8e tools/convert/Sbml2Graph/Sbml2Graph.xml
--- a/tools/convert/Sbml2Graph/Sbml2Graph.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/convert/Sbml2Graph/Sbml2Graph.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="0.11.0">
+<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="0.12.0">
   <description>Create a graph representation of a SBML file content, and export it in graph file format.</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 convert.Sbml2Graph -i "$inputPath"
  $bipartite
@@ -58,4 +58,5 @@
   </tests>
   <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
 The graph can be either a compound graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/convert/Sbml2Tab/Sbml2Tab.xml
--- a/tools/convert/Sbml2Tab/Sbml2Tab.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/convert/Sbml2Tab/Sbml2Tab.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="0.11.0">
+<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="0.12.0">
   <description>Create a tabulated file from a SBML file</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i):
  -i "$i"
@@ -59,4 +59,5 @@
     </test>
   </tests>
   <help><![CDATA[Create a tabulated file from a SBML file]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/convert/Tab2Sbml/Tab2Sbml.xml
--- a/tools/convert/Tab2Sbml/Tab2Sbml.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/convert/Tab2Sbml/Tab2Sbml.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="0.11.0">
+<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="0.12.0">
   <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan':
  -ci "$colid"
@@ -138,4 +138,5 @@
     </test>
   </tests>
   <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/met4j.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/met4j.yml	Mon Jun 27 13:41:08 2022 +0000
@@ -0,0 +1,92 @@
+---
+install_repository_dependencies: true
+install_resolver_dependencies: true
+install_tool_dependencies: false
+tools:
+  - name: ExtractPathways
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: ExtractSbmlAnnot
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: SbmlSetChargesFromFile
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: SbmlSetEcsFromFile
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: SbmlSetFormulasFromFile
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: SbmlSetGprsFromFile
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: SbmlSetNamesFromFile
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: SbmlSetPathwaysFromFile
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: SbmlSetRefsFromFile
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: SbmlToMetaboliteTable
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: GetModelProteome
+    owner: metexplore
+    tool_panel_section_id: met4j_bigg
+  - name: FbcToNotes
+    owner: metexplore
+    tool_panel_section_id: met4j_convert
+  - name: Kegg2Sbml
+    owner: metexplore
+    tool_panel_section_id: met4j_convert
+  - name: Sbml2Graph
+    owner: metexplore
+    tool_panel_section_id: met4j_convert
+  - name: Sbml2Tab
+    owner: metexplore
+    tool_panel_section_id: met4j_convert
+  - name: Tab2Sbml
+    owner: metexplore
+    tool_panel_section_id: met4j_convert
+  - name: CarbonSkeletonNet
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: ChokePoint
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: CompoundNet
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: DistanceMatrix
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: ExtractSubBipNetwork
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: ExtractSubNetwork
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: ExtractSubReactionNetwork
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: LoadPoint
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: MetaboRank
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: NetworkSummary
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: PrecursorNetwork
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: ScopeNetwork
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
+  - name: SideCompoundsScan
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml
--- a/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="0.11.0">
+<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="0.12.0">
   <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</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.CarbonSkeletonNet -s "$inputPath"
  -g "$inputAAM"
@@ -116,4 +116,5 @@
     </test>
   </tests>
   <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produce a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) perform atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ChokePoint/ChokePoint.xml
--- a/tools/networkAnalysis/ChokePoint/ChokePoint.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/ChokePoint/ChokePoint.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ChokePoint" name="ChokePoint" version="0.11.0">
+<tool id="met4j_ChokePoint" name="ChokePoint" version="0.12.0">
   <description>Compute the Choke points of a metabolic network.</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.ChokePoint -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
@@ -48,4 +48,5 @@
   <help><![CDATA[Compute the Choke points of a metabolic network.
 Load points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target 
 See : Syed Asad Rahman, Dietmar Schomburg; Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinformatics 2006; 22 (14): 1767-1774. doi: 10.1093/bioinformatics/btl181]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/CompoundNet/CompoundNet.xml
--- a/tools/networkAnalysis/CompoundNet/CompoundNet.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/CompoundNet/CompoundNet.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_CompoundNet" name="CompoundNet" version="0.11.0">
+<tool id="met4j_CompoundNet" name="CompoundNet" version="0.12.0">
   <description>Advanced creation of a compound graph representation of a SBML file content</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath"
 #if str($inputSide) != 'None':
@@ -74,4 +74,5 @@
   <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes.
 While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations.
 In contrary to the SBML2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree² weighting to get relevant structure without structural data.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml
--- a/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,15 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="0.11.0">
+<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="0.12.0">
   <description>Create a compound to compound distance matrix.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
- -s "$sideCompoundFile"
+ -sc "$sideCompoundFile"
+#end if
+#if str($seedFile) != 'None':
+ -s "$seedFile"
 #end if
  $degree
 #if str($weightFile) != 'None':
@@ -20,7 +23,8 @@
 ]]></command>
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
-    <param argument="-s" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
+    <param argument="-sc" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
+    <param argument="-s" format="text" label="an optional file containing list of compounds of interest. The returned distance matrix contains only the corresponding rows and columns" name="seedFile" optional="true" type="data" value=""/>
     <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting (-w must not be set)" name="degree" truevalue="-dw" type="boolean" value="false"/>
     <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
     <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
@@ -55,4 +59,5 @@
 The distance between two compounds is computed as the length of the shortest path connecting the two in the compound graph, where two compounds are linked if they are respectively substrate and product of the same reaction.
 An optional edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path.The default weighting use target's degree squared. Alternatively, custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.
 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="0.12.0">
+  <description>Create a subnetwork from a GSMN 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.</description>
+  <xrefs>
+    <xref type="bio.tools">met4j</xref>
+  </xrefs>
+  <requirements>
+    <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.ExtractSubBipNetwork -i "$inputPath"
+ -s "$sourcePath"
+ -t "$targetPath"
+ $undirected
+ $asTable
+ -sc "$sideCompoundFile"
+#if str($blkdReactionFile) != 'None':
+ -br "$blkdReactionFile"
+#end if
+#if str($weightFile) != 'None':
+ -cw "$weightFile"
+#end if
+#if str($k):
+ -k "$k"
+#end if
+ $st
+ -o "$outputPath"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
+    <param argument="-s" format="text" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
+    <param argument="-t" format="text" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
+    <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
+    <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
+    <param argument="-sc" format="text" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/>
+    <param argument="-br" format="text" label="a file containing list of blocked reactions to ignore" name="blkdReactionFile" optional="true" type="data" value=""/>
+    <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/>
+    <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+    <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/>
+  </inputs>
+  <outputs>
+    <data format="gml" name="outputPath"/>
+  </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"/>
+        <output ftype="gml" name="outputPath">
+          <assert_contents>
+            <has_line_matching expression=".*node.*" n="5"/>
+            <has_line_matching expression=".*edge.*" n="4"/>
+          </assert_contents>
+        </output>
+      </test>
+
+  </tests>
+  <help><![CDATA[Create a subnetwork from a GSMN 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 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.]]></help>
+  <citations/>
+</tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ExtractSubBipNetwork/test-data/sc.txt
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ExtractSubBipNetwork/test-data/seeds.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/test-data/seeds.txt	Mon Jun 27 13:41:08 2022 +0000
@@ -0,0 +1,1 @@
+A
\ No newline at end of file
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ExtractSubBipNetwork/test-data/targets.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/test-data/targets.txt	Mon Jun 27 13:41:08 2022 +0000
@@ -0,0 +1,1 @@
+D
\ No newline at end of file
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ExtractSubBipNetwork/test-data/test.gml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/test-data/test.gml	Mon Jun 27 13:41:08 2022 +0000
@@ -0,0 +1,56 @@
+Creator "JGraphT GML Exporter"
+Version 1
+graph
+[
+	label ""
+	directed 1
+	node
+	[
+		id 1
+		label "A"
+	]
+	node
+	[
+		id 2
+		label "reac2"
+	]
+	node
+	[
+		id 3
+		label "B"
+	]
+	node
+	[
+		id 4
+		label "reac4"
+	]
+	node
+	[
+		id 5
+		label "D"
+	]
+	edge
+	[
+		source 1
+		target 2
+		label "(A : reac2)"
+	]
+	edge
+	[
+		source 2
+		target 3
+		label "(reac2 : B)"
+	]
+	edge
+	[
+		source 3
+		target 4
+		label "(B : reac4)"
+	]
+	edge
+	[
+		source 4
+		target 5
+		label "(reac4 : D)"
+	]
+]
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ExtractSubBipNetwork/test-data/toy_model.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/test-data/toy_model.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -0,0 +1,119 @@
+<?xml version="1.0" encoding='UTF-8' ?>
+<sbml fbc:required="false" groups:required="false" level="3" version="1"
+	xmlns="http://www.sbml.org/sbml/level3/version1/core"
+	xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"
+	xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1">
+	<model fbc:strict="true" name="toy model">
+		<listOfUnitDefinitions>
+			<unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
+				<listOfUnits>
+					<unit exponent="-1" kind="gram" multiplier="1" scale="0"/>
+					<unit exponent="1" kind="mole" multiplier="1" scale="-3"/>
+					<unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/>
+				</listOfUnits>
+			</unitDefinition>
+		</listOfUnitDefinitions>
+		<listOfCompartments>
+			<compartment constant="false" id="c" name="Cytosol"/>
+			<compartment constant="false" id="e" name="Extracellular"/>
+		</listOfCompartments>
+		<listOfSpecies>
+			<species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext">
+				<notes>
+					<body xmlns="http://www.w3.org/1999/xhtml">
+						<p>SMILES: C[C@@H](C(=O)O)NC</p>
+					</body>
+				</notes>
+				<annotation>
+					<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+						xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+						<rdf:Description rdf:about="#A_ext">
+							<bqbiol:is>
+								<in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi>
+							</bqbiol:is>
+						</rdf:Description>
+					</rdf:RDF>
+				</annotation>
+
+			</species>
+			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/>
+			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/>
+			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/>
+			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/>
+			<species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/>
+			<species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/>
+			<species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/>
+		</listOfSpecies>
+		<listOfParameters>
+			<parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/>
+			<parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/>
+			<parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/>
+			<parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/>
+			<parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/>
+			<parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+			<parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+			<parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+			<parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+			<parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+		</listOfParameters>
+		<listOfReactions>
+			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false">
+				<listOfReactants>
+					<speciesReference constant="true" species="A_ext" stoichiometry="1.0"/>
+				</listOfReactants>
+				<listOfProducts>
+					<speciesReference constant="true" species="A" stoichiometry="1.0"/>
+				</listOfProducts>
+			</reaction>
+			<reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true">
+				<listOfReactants>
+					<speciesReference constant="true" species="A" stoichiometry="1.0"/>
+				</listOfReactants>
+				<listOfProducts>
+					<speciesReference constant="true" species="B" stoichiometry="1.0"/>
+				</listOfProducts>
+			</reaction>
+			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false">
+				<listOfReactants>
+					<speciesReference constant="true" species="A" stoichiometry="1.0"/>
+				</listOfReactants>
+				<listOfProducts>
+					<speciesReference constant="true" species="C" stoichiometry="1.0"/>
+				</listOfProducts>
+			</reaction>
+			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false">
+				<listOfReactants>
+					<speciesReference constant="true" species="B" stoichiometry="1.0"/>
+					<speciesReference constant="true" species="C" stoichiometry="1.0"/>
+				</listOfReactants>
+				<listOfProducts>
+					<speciesReference constant="true" species="D" stoichiometry="1.5"/>
+				</listOfProducts>
+			</reaction>
+			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false">
+				<listOfReactants>
+					<speciesReference constant="true" species="D" stoichiometry="1.0"/>
+				</listOfReactants>
+				<listOfProducts>
+					<speciesReference constant="true" species="D_ext" stoichiometry="1.0"/>
+				</listOfProducts>
+			</reaction>
+			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false">
+				<listOfReactants>
+					<speciesReference constant="true" species="E_ext" stoichiometry="1.0"/>
+				</listOfReactants>
+				<listOfProducts>
+					<speciesReference constant="true" species="E" stoichiometry="1.0"/>
+				</listOfProducts>
+			</reaction>
+			<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false">
+				<listOfReactants>
+					<speciesReference constant="true" species="E" stoichiometry="2.0"/>
+				</listOfReactants>
+				<listOfProducts>
+					<speciesReference constant="true" species="D" stoichiometry="1.0"/>
+				</listOfProducts>
+			</reaction>
+		</listOfReactions>
+	</model>
+</sbml>
\ No newline at end of file
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml
--- a/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="0.11.0">
+<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="0.12.0">
   <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row.</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.ExtractSubNetwork -i "$inputPath"
  -s "$sourcePath"
@@ -18,6 +18,8 @@
  -cw "$weightFile"
 #end if
  $chemicalSim
+ $undirected
+ $asTable
 #if str($k):
  -k "$k"
 #end if
@@ -32,6 +34,8 @@
     <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/>
     <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
     <param argument="-sw" checked="false" falsevalue="" label="penalize traversal of non-relevant edges by using chemical similarity weighting" name="chemicalSim" truevalue="-sw" type="boolean" value="false"/>
+    <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
+    <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
     <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
@@ -67,4 +71,5 @@
 Pertusi DA, Stine AE, Broadbelt LJ, et al. Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics 2014;1–9.
 McShan DC, Rao S, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics 2003;19:1692–8.
 ]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml
--- a/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,14 +1,16 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="0.11.0">
+<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="0.12.0">
   <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</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.ExtractSubReactionNetwork -i "$inputPath"
  -s "$sourcePath"
+ $undirected
+ $asTable
  -t "$targetPath"
  -sc "$sideCompoundFile"
 #if str($weightFile) != 'None':
@@ -23,6 +25,8 @@
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
     <param argument="-s" format="text" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
+    <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
+    <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
     <param argument="-t" format="text" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
     <param argument="-sc" format="text" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/>
     <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/>
@@ -53,4 +57,5 @@
   <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
 The subnetwork corresponds to part of the network that connects reactions from the first list to reactions 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, reaction graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds to ignore for linking reactions must be provided. An optional edge weight file, if available, can also be used.]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/LoadPoint/LoadPoint.xml
--- a/tools/networkAnalysis/LoadPoint/LoadPoint.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/LoadPoint/LoadPoint.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_LoadPoint" name="LoadPoint" version="0.11.0">
+<tool id="met4j_LoadPoint" name="LoadPoint" version="0.12.0">
   <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug target.</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.LoadPoint -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
@@ -48,4 +48,5 @@
 P is the total number of shortest paths;
 K is the sum of links in the metabolic network of M metabolites (where M is the number of metabolites in the network).
 Use of the logarithm makes the relevant values more distinguishable.]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/MetaboRank/MetaboRank.xml
--- a/tools/networkAnalysis/MetaboRank/MetaboRank.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/MetaboRank/MetaboRank.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_MetaboRank" name="MetaboRank" version="0.11.0">
+<tool id="met4j_MetaboRank" name="MetaboRank" version="0.12.0">
   <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</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.MetaboRank -i "$sbmlFilePath"
  -s "$seedsFilePath"
@@ -50,4 +50,5 @@
 The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining.
 It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks.
 See publication for more information: Frainay et al. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results, Bioinformatics (35-2), https://doi.org/10.1093/bioinformatics/bty577]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/NetworkSummary/NetworkSummary.xml
--- a/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_NetworkSummary" name="NetworkSummary" version="0.11.0">
+<tool id="met4j_NetworkSummary" name="NetworkSummary" version="0.12.0">
   <description>Create a report summarizing several graph measures characterising the structure of the network.</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.NetworkSummary -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
@@ -32,4 +32,5 @@
     </test>
   </tests>
   <help><![CDATA[Use a metabolic network in SBML file and an optional list of side compounds, and produce a report summarizing several graph measures characterising the structure of the network.This includes (non-exhaustive list): size and order, connectivity, density, degree distribution, shortest paths length, top centrality nodes...]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml
--- a/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="0.11.0">
+<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="0.12.0">
   <description>Perform a network expansion from a set of compound targets to create a precursor network.</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.PrecursorNetwork -i "$sbmlFilePath"
  -t "$targetsFilePath"
@@ -16,7 +16,7 @@
  -ir "$reactionToIgnoreFile"
 #end if
  -o "$output"
-]]>  </command>
+]]></command>
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file: path to network used for computing scope, in sbml format." name="sbmlFilePath" optional="false" type="data" value=""/>
     <param argument="-t" format="" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/>
@@ -40,4 +40,5 @@
   </tests>
   <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network.
 The precursor network of a set of compounds (targets) refer to the sub-part of a metabolic network from which a target can be reachedThe network expansion process consist of adding a reaction to the network if any of its products are either a targets or a substrate of a previously added reaction]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml
--- a/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="0.11.0">
+<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="0.12.0">
   <description>Perform a network expansion from a set of compound seeds to create a scope network</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.ScopeNetwork -i "$sbmlFilePath"
  -s "$seedsFilePath"
@@ -46,4 +46,5 @@
   <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network
 The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction
 For more information, see Handorf, Ebenhöh and Heinrich (2005). *Expanding metabolic networks: scopes of compounds, robustness, and evolution.* Journal of molecular evolution, 61(4), 498-512. (https://doi.org/10.1007/s00239-005-0027-1)]]></help>
+  <citations/>
 </tool>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml
--- 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>
diff -r dcd16521b969 -r 9b162ee6ff8e tools/tool_conf.xml
--- a/tools/tool_conf.xml	Fri Jun 10 10:31:34 2022 +0000
+++ b/tools/tool_conf.xml	Mon Jun 27 13:41:08 2022 +0000
@@ -1,37 +1,37 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <toolbox monitor="true">
-  <section id="met4j" name="met4j apps">
-    <label id="attributes" text="met4j attributes" version=""/>
-    <tool file="met4j/attributes/ExtractPathways/ExtractPathways.xml"/>
-    <tool file="met4j/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml"/>
-    <tool file="met4j/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml"/>
-    <tool file="met4j/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml"/>
-    <tool file="met4j/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml"/>
-    <tool file="met4j/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml"/>
-    <tool file="met4j/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml"/>
-    <tool file="met4j/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml"/>
-    <tool file="met4j/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml"/>
-    <tool file="met4j/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml"/>
-    <label id="bigg" text="met4j bigg" version=""/>
-    <tool file="met4j/bigg/GetModelProteome/GetModelProteome.xml"/>
-    <label id="convert" text="met4j convert" version=""/>
-    <tool file="met4j/convert/FbcToNotes/FbcToNotes.xml"/>
-    <tool file="met4j/convert/Kegg2Sbml/Kegg2Sbml.xml"/>
-    <tool file="met4j/convert/Sbml2Graph/Sbml2Graph.xml"/>
-    <tool file="met4j/convert/Sbml2Tab/Sbml2Tab.xml"/>
-    <tool file="met4j/convert/Tab2Sbml/Tab2Sbml.xml"/>
-    <label id="networkAnalysis" text="met4j networkAnalysis" version=""/>
-    <tool file="met4j/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml"/>
-    <tool file="met4j/networkAnalysis/ChokePoint/ChokePoint.xml"/>
-    <tool file="met4j/networkAnalysis/CompoundNet/CompoundNet.xml"/>
-    <tool file="met4j/networkAnalysis/DistanceMatrix/DistanceMatrix.xml"/>
-    <tool file="met4j/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml"/>
-    <tool file="met4j/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml"/>
-    <tool file="met4j/networkAnalysis/LoadPoint/LoadPoint.xml"/>
-    <tool file="met4j/networkAnalysis/MetaboRank/MetaboRank.xml"/>
-    <tool file="met4j/networkAnalysis/NetworkSummary/NetworkSummary.xml"/>
-    <tool file="met4j/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml"/>
-    <tool file="met4j/networkAnalysis/ScopeNetwork/ScopeNetwork.xml"/>
-    <tool file="met4j/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml"/>
-  </section>
+  <label id="met4j" text="MET4J"/>
+  <section id="met4j_attributes" name="Met4J - attributes"/>
+  <tool file="met4j/attributes/ExtractPathways/ExtractPathways.xml"/>
+  <tool file="met4j/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml"/>
+  <tool file="met4j/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml"/>
+  <tool file="met4j/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml"/>
+  <tool file="met4j/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml"/>
+  <tool file="met4j/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml"/>
+  <tool file="met4j/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml"/>
+  <tool file="met4j/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml"/>
+  <tool file="met4j/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml"/>
+  <tool file="met4j/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml"/>
+  <section id="met4j_bigg" name="Met4J - bigg"/>
+  <tool file="met4j/bigg/GetModelProteome/GetModelProteome.xml"/>
+  <section id="met4j_convert" name="Met4J - convert"/>
+  <tool file="met4j/convert/FbcToNotes/FbcToNotes.xml"/>
+  <tool file="met4j/convert/Kegg2Sbml/Kegg2Sbml.xml"/>
+  <tool file="met4j/convert/Sbml2Graph/Sbml2Graph.xml"/>
+  <tool file="met4j/convert/Sbml2Tab/Sbml2Tab.xml"/>
+  <tool file="met4j/convert/Tab2Sbml/Tab2Sbml.xml"/>
+  <section id="met4j_networkanalysis" name="Met4J - networkAnalysis"/>
+  <tool file="met4j/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml"/>
+  <tool file="met4j/networkAnalysis/ChokePoint/ChokePoint.xml"/>
+  <tool file="met4j/networkAnalysis/CompoundNet/CompoundNet.xml"/>
+  <tool file="met4j/networkAnalysis/DistanceMatrix/DistanceMatrix.xml"/>
+  <tool file="met4j/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml"/>
+  <tool file="met4j/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml"/>
+  <tool file="met4j/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml"/>
+  <tool file="met4j/networkAnalysis/LoadPoint/LoadPoint.xml"/>
+  <tool file="met4j/networkAnalysis/MetaboRank/MetaboRank.xml"/>
+  <tool file="met4j/networkAnalysis/NetworkSummary/NetworkSummary.xml"/>
+  <tool file="met4j/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml"/>
+  <tool file="met4j/networkAnalysis/ScopeNetwork/ScopeNetwork.xml"/>
+  <tool file="met4j/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml"/>
 </toolbox>