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changeset 2:e69a78624877 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
author metexplore
date Tue, 19 Jul 2022 14:20:07 +0000
parents 9b162ee6ff8e
children 6bd9aad9626d
files tools/attributes/ExtractPathways/ExtractPathways.xml tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml tools/bigg/GetModelProteome/GetModelProteome.xml tools/convert/FbcToNotes/FbcToNotes.xml tools/convert/Kegg2Sbml/Kegg2Sbml.xml tools/convert/Sbml2Graph/Sbml2Graph.xml tools/convert/Sbml2Tab/Sbml2Tab.xml tools/convert/Tab2Sbml/Tab2Sbml.xml tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml tools/networkAnalysis/ChokePoint/ChokePoint.xml tools/networkAnalysis/CompoundNet/CompoundNet.xml tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml tools/networkAnalysis/LoadPoint/LoadPoint.xml tools/networkAnalysis/MetaboRank/MetaboRank.xml tools/networkAnalysis/NetworkSummary/NetworkSummary.xml tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml
diffstat 29 files changed, 81 insertions(+), 84 deletions(-) [+]
line wrap: on
line diff
--- a/tools/attributes/ExtractPathways/ExtractPathways.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/ExtractPathways/ExtractPathways.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractPathways" name="ExtractPathways" version="0.12.0">
+<tool id="met4j_ExtractPathways" name="ExtractPathways" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath"
  -p "$pathwayId"
--- a/tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="0.12.0">
+<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractSbmlAnnot -i "$inputPath"
  -export "$export"
--- a/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="0.12.0">
+<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan':
  -cc "$colcharge"
--- a/tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.12.0">
+<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetEcsFromFile#if str($colec) != 'nan':
  -cec "$colec"
--- a/tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="0.12.0">
+<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan':
  -cf "$colformula"
--- a/tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.12.0">
+<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan':
  -cgpr "$colgpr"
--- a/tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="0.12.0">
+<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetNamesFromFile#if str($colname) != 'nan':
  -cname "$colname"
--- a/tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.12.0">
+<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan':
  -cp "$colp"
@@ -62,9 +62,9 @@
       <assert_contents>
         <is_valid_xml/>
         <has_line_matching expression=".*groups:id=.*" n="3"/>
-        <has_line_matching expression=".*groups:id=.P1.*" n="1"/>
-        <has_line_matching expression=".*groups:id=.P2.*" n="1"/>
-        <has_line_matching expression=".*groups:id=.P3.*" n="1"/>
+        <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
+        <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
+        <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
       </assert_contents>
     </output>
     </test>
@@ -76,9 +76,9 @@
       <assert_contents>
         <is_valid_xml/>
         <has_line_matching expression=".*groups:id=.*" n="3"/>
-        <has_line_matching expression=".*groups:id=.P1.*" n="1"/>
-        <has_line_matching expression=".*groups:id=.P2.*" n="1"/>
-        <has_line_matching expression=".*groups:id=.P3.*" n="1"/>
+        <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
+        <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
+        <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
       </assert_contents>
     </output>
     </test>
--- a/tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="0.12.0">
+<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan':
  -cr "$colRef"
--- a/tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="0.12.0">
+<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlToMetaboliteTable -s "$sbml"
  -o "$outputFile"
--- a/tools/bigg/GetModelProteome/GetModelProteome.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/bigg/GetModelProteome/GetModelProteome.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_GetModelProteome" name="GetModelProteome" version="0.12.0">
+<tool id="met4j_GetModelProteome" name="GetModelProteome" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetModelProteome -m "$modelId"
  -o "$outputFile"
--- a/tools/convert/FbcToNotes/FbcToNotes.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/convert/FbcToNotes/FbcToNotes.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_FbcToNotes" name="FbcToNotes" version="0.12.0">
+<tool id="met4j_FbcToNotes" name="FbcToNotes" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath"
  -o "$outputPath"
--- a/tools/convert/Kegg2Sbml/Kegg2Sbml.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/convert/Kegg2Sbml/Kegg2Sbml.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="0.12.0">
+<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org):
  -org "$org"
--- a/tools/convert/Sbml2Graph/Sbml2Graph.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/convert/Sbml2Graph/Sbml2Graph.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="0.12.0">
+<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
  $bipartite
@@ -24,7 +24,7 @@
     <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/>
   </inputs>
   <outputs>
-    <data format="text" name="outputPath"/>
+    <data format="txt" name="outputPath"/>
   </outputs>
   <tests>
     <test>
--- a/tools/convert/Sbml2Tab/Sbml2Tab.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/convert/Sbml2Tab/Sbml2Tab.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="0.12.0">
+<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="1.0.1">
   <description>Create a tabulated file from a SBML file</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i):
  -i "$i"
--- a/tools/convert/Tab2Sbml/Tab2Sbml.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/convert/Tab2Sbml/Tab2Sbml.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="0.12.0">
+<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.0.1">
   <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan':
  -ci "$colid"
@@ -24,9 +24,7 @@
 #if str($r):
  -r "$r"
 #end if
-#if str($in) != 'None':
  -in "$in"
-#end if
 #if str($id):
  -id "$id"
 #end if
@@ -59,7 +57,7 @@
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
-    <param argument="-in" format="tsv" label="Tabulated file" name="in" optional="true" type="data" value=""/>
+    <param argument="-in" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/>
     <param argument="-id" label="[NA] Model id written in the SBML file" name="id" optional="true" type="text" value="NA">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
--- a/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="0.12.0">
+<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.0.1">
   <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath"
  -g "$inputAAM"
--- a/tools/networkAnalysis/ChokePoint/ChokePoint.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/ChokePoint/ChokePoint.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ChokePoint" name="ChokePoint" version="0.12.0">
+<tool id="met4j_ChokePoint" name="ChokePoint" version="1.0.1">
   <description>Compute the Choke points of a metabolic network.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
@@ -15,7 +15,7 @@
 ]]></command>
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
-    <param argument="-s" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
+    <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
   </inputs>
   <outputs>
     <data format="tsv" name="outputPath"/>
--- a/tools/networkAnalysis/CompoundNet/CompoundNet.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/CompoundNet/CompoundNet.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_CompoundNet" name="CompoundNet" version="0.12.0">
+<tool id="met4j_CompoundNet" name="CompoundNet" version="1.0.1">
   <description>Advanced creation of a compound graph representation of a SBML file content</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath"
 #if str($inputSide) != 'None':
--- a/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="0.12.0">
+<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="1.0.1">
   <description>Create a compound to compound distance matrix.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
@@ -23,8 +23,8 @@
 ]]></command>
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" 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="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
+    <param argument="-s" format="txt" 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"/>
--- a/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="0.12.0">
+<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="1.0.1">
   <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>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath"
  -s "$sourcePath"
@@ -27,12 +27,12 @@
 ]]></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="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
+    <param argument="-t" format="txt" 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="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/>
+    <param argument="-br" format="txt" 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="_">
@@ -45,7 +45,7 @@
     <data format="gml" name="outputPath"/>
   </outputs>
   <tests>
-      <test>
+    <test>
         <param name="inputPath" value="toy_model.xml"/>
         <param name="sourcePath" value="seeds.txt"/>
         <param name="targetPath" value="targets.txt"/>
@@ -57,7 +57,6 @@
           </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.
--- a/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="0.12.0">
+<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath"
  -s "$sourcePath"
@@ -28,9 +28,9 @@
 ]]></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="-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="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
+    <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
+    <param argument="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
     <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"/>
--- a/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="0.12.0">
+<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
  -s "$sourcePath"
@@ -24,11 +24,11 @@
 ]]></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="-s" format="txt" 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="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
+    <param argument="-sc" format="txt" 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=""/>
     <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1">
       <sanitizer invalid_char="_">
--- a/tools/networkAnalysis/LoadPoint/LoadPoint.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/LoadPoint/LoadPoint.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_LoadPoint" name="LoadPoint" version="0.12.0">
+<tool id="met4j_LoadPoint" name="LoadPoint" version="1.0.1">
   <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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
@@ -18,7 +18,7 @@
 ]]></command>
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
-    <param argument="-s" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
+    <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
     <param argument="-k" label="Number of alternative paths to consider between a pair of connected metabolites" name="k" optional="true" type="text" value="1">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
--- a/tools/networkAnalysis/MetaboRank/MetaboRank.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/MetaboRank/MetaboRank.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_MetaboRank" name="MetaboRank" version="0.12.0">
+<tool id="met4j_MetaboRank" name="MetaboRank" version="1.0.1">
   <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath"
  -s "$seedsFilePath"
--- a/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_NetworkSummary" name="NetworkSummary" version="0.12.0">
+<tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.0.1">
   <description>Create a report summarizing several graph measures characterising the structure of the network.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
--- a/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="0.12.0">
+<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.0.1">
   <description>Perform a network expansion from a set of compound targets to create a precursor network.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath"
  -t "$targetsFilePath"
--- a/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="0.12.0">
+<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.0.1">
   <description>Perform a network expansion from a set of compound seeds to create a scope network</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
  -s "$seedsFilePath"
--- a/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="0.12.0">
+<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="1.0.1">
   <description>Scan a network to identify side-compounds.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath"
  $sideOnly