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Changeset 3:6bd9aad9626d (2022-07-29)

Previous changeset 2:e69a78624877 (2022-07-19) Next changeset 4:ae4c301919c4 (2022-11-17)

Commit message:
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414

diff -r e69a78624877 -r 6bd9aad9626d data/XF_network_R_Seed.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/XF_network_R_Seed.tab Fri Jul 29 13:23:40 2022 +0000

@@ -0,0 +1,2 @@
+R_ACGS
+R_GLUN

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/DecomposeSBML/DecomposeSBML.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/DecomposeSBML/DecomposeSBML.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_DecomposeSBML" name="DecomposeSBML" version="1.1.0">
+ <description>Parse SBML to render list of composing entities: metabolites, reactions, genes and others.</description>
+ <xrefs>
+ <xref type="bio.tools">met4j</xref>
+ </xrefs>
+ <requirements>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ </requirements>
+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.DecomposeSBML -i "$sbml"
+ $printMetabolites
+ $printReactions
+ $printCompartments
+ $printPathways
+ $printGenes
+ $noTypeCol
+ -o "$outputFile"
+]]></command>
+ <inputs>
+ <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
+ <param argument="-m" checked="false" falsevalue="" label="Extract Metabolites" name="printMetabolites" truevalue="-m" type="boolean" value="false"/>
+ <param argument="-r" checked="false" falsevalue="" label="Extract Reactions" name="printReactions" truevalue="-r" type="boolean" value="false"/>
+ <param argument="-c" checked="false" falsevalue="" label="Extract Compartments" name="printCompartments" truevalue="-c" type="boolean" value="false"/>
+ <param argument="-p" checked="false" falsevalue="" label="Extract Pathways" name="printPathways" truevalue="-p" type="boolean" value="false"/>
+ <param argument="-g" checked="false" falsevalue="" label="Extract Genes" name="printGenes" truevalue="-g" type="boolean" value="false"/>
+ <param argument="-nt" checked="false" falsevalue="" label="Do not output type column" name="noTypeCol" truevalue="-nt" type="boolean" value="false"/>
+ </inputs>
+ <outputs>
+ <data format="tsv" name="outputFile"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="sbml" value="Human-GEM_pathways.xml"/>
+ <output ftype="tsv" name="outputFile">
+ <assert_contents>
+ <has_text_matching expression="GENE" n="86"/>
+ <has_text_matching expression="METABOLITE" n="111"/>
+ <has_text_matching expression="REACTION" n="75"/>
+ <has_text_matching expression="PATHWAY" n="3"/>
+ <has_text_matching expression="COMPARTMENT" n="5"/>
+ </assert_contents>
+ </output>
+ </test>
+ <test>
+ <param name="sbml" value="Human-GEM_pathways.xml"/>
+ <param name="printReactions" value="true"/>
+ <param name="printMetabolites" value="true"/>
+ <param name="printGenes" value="true"/>
+ <param name="printCompartments" value="true"/>
+ <param name="noTypeCol" value="true"/>
+ <output ftype="tsv" name="outputFile">
+ <assert_contents>
+ <has_n_lines n="277"/>
+ </assert_contents>
+ </output>
+ </test>
+ </tests>
+ <help><![CDATA[Parse SBML to render list of composing entities: metabolites, reactions, genes, pathways and compartments. The output file is a tsv with two columns, one with entities identifiers, and one with the entity type. If no entity type is selected, by default all of them are taken into account. Only identifiers are written, attributes can be extracted from dedicated apps or from the SBML2Tab.]]></help>
+ <citations/>
+</tool>

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/DecomposeSBML/test-data/Human-GEM_pathways.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/DecomposeSBML/test-data/Human-GEM_pathways.xml Fri Jul 29 13:23:40 2022 +0000

b'@@ -0,0 +1,7661 @@\n+<?xml version="1.0" encoding="UTF-8"?>\r\n+<sbml fbc:required="false" groups:required="false" level="3" version="2" xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1">\r\n+ <model fbc:strict="true" id="HumanGEM" metaid="HumanGEM" name="Generic genome-scale metabolic model of Homo sapiens">\r\n+ <notes>\r\n+ <body xmlns="http://www.w3.org/1999/xhtml">\r\n+ Genome-scale metabolic models are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. This is the latest version of Human-GEM, which is a genome-scale metabolic model of a generic human cell. The objective of Human-GEM is to serve as a community model for enabling integrative and mechanistic studies of human metabolism.\r\n+ </body>\r\n+ </notes>\r\n+ <annotation>\r\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\r\n+ <rdf:Description rdf:about="#HumanGEM">\r\n+ <bqbiol:is>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/taxonomy/9606"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:is>\r\n+ </rdf:Description>\r\n+ </rdf:RDF>\r\n+ </annotation>\r\n+ <fbc:listOfObjectives fbc:activeObjective="obj">\r\n+ <fbc:objective fbc:id="obj" fbc:type="maximize">\r\n+ <fbc:listOfFluxObjectives>\r\n+ <fbc:fluxObjective fbc:coefficient="1" fbc:reaction="R_biomass_human"/>\r\n+ </fbc:listOfFluxObjectives>\r\n+ </fbc:objective>\r\n+ </fbc:listOfObjectives>\r\n+ <fbc:listOfGeneProducts>\r\n+ <fbc:geneProduct fbc:id="ENSG00000023697" fbc:label="ENSG00000023697" fbc:name="ENSG00000023697" metaid="_12915ddf-e017-4a38-a80d-e9982f8ac7cc">\r\n+ <notes>\r\n+ <body xmlns="http://www.w3.org/1999/xhtml">\r\n+ ensembl: ENSG00000023697\r\n+ hgnc.symbol: DERA\r\n+ ncbigene: 51071\r\n+ uniprot: Q9Y315\r\n+ </body>\r\n+ </notes>\r\n+ </fbc:geneProduct>\r\n+ <fbc:geneProduct fbc:id="ENSG00000130313" fbc:label="ENSG00000130313" fbc:name="ENSG00000130313" metaid="b7f31dab-0da6-4c9e-9c76-6ea1952d4f6b">\r\n+ <notes>\r\n+ <body xmlns="http://www.w3.org/1999/xhtml">\r\n+ ensembl: ENSG00000130313\r\n+ hgnc.symbol: PGLS\r\n+ ncbigene: 25796\r\n+ uniprot: O95336\r\n+ </body>\r\n+ </notes>\r\n+ </fbc:geneProduct>\r\n+ <fbc:geneProduct fbc:id="ENSG00000157353" fbc:label="ENSG00000157353" fbc:name="ENSG00000157353" metaid="f2bfd1a8-b479-4718-bb3f-030aed87a562">\r\n+ <notes>\r\n+ <body xmlns="http://www.w3.org/1999/xhtml">\r\n+ ensembl: ENSG00000157353\r\n+ hgnc.symbol: FCSK\r\n+ ncbigene: 197258\r\n+ uniprot: Q8N0W3\r\n+ </body>\r\n+ </notes>\r\n+ </fbc:geneProduct>\r\n+ <fbc:geneProduct fbc:id="ENSG00000114268" fbc:label="ENSG00000114268" fbc:name="ENSG00000114268" metaid="d1ad0711-77a6-4e33-85ba-dff0e0e56b5c">\r\n+ <notes>\r\n+ <body xmlns="http://www.w3.org/1999/xhtml">\r\n+ ensembl: ENSG00000114268\r\n+ hgnc.symbol: PFKFB4\r\n+ ncbigene: 5210\r\n+ uniprot: Q16877\r\n+ </body>\r\n+ </notes>\r\n+ </fbc:geneProduct>\r\n+ <fbc:geneProduct fbc:id="ENSG00000197417" fbc:label="ENSG00000197417" fbc:name="ENSG00000197417" metaid="_36aac772-72a3-44fd-97f3-84213d36d9e2">\r\n+ <notes>\r\n+ <body xmlns="http://www.w3.org/1999/xhtml">\r\n+ ensembl: ENSG00000197417\r\n+ hgnc.symbol: SHPK\r\n+ ncbigene: 23729\r\n+ uniprot: Q9UHJ6\r\n+ </body>\r\n+ </notes>\r\n+ </fbc:geneProduct>\r\n+ '..b' </rdf:Bag>\r\n+ </bqbiol:is>\r\n+ <bqbiol:isDescribedBy>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/pubmed/234468"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/pubmed/2843500"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/pubmed/15234337"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:isDescribedBy>\r\n+ </rdf:Description>\r\n+ </rdf:RDF>\r\n+ </annotation>\r\n+ <fbc:geneProductAssociation>\r\n+ <fbc:or>\r\n+ <fbc:geneProductRef fbc:geneProduct="ENSG00000197713"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="ENSG00000235376"/>\r\n+ </fbc:or>\r\n+ </fbc:geneProductAssociation>\r\n+ <listOfReactants>\r\n+ <speciesReference constant="true" species="M_m01761c" stoichiometry="1"/>\r\n+ </listOfReactants>\r\n+ <listOfProducts>\r\n+ <speciesReference constant="true" species="M_m02846c" stoichiometry="1"/>\r\n+ </listOfProducts>\r\n+ </reaction>\r\n+ <reaction fbc:lowerFluxBound="LOWER_BOUND_0_0" fbc:upperFluxBound="UPPER_BOUND_1000_0" id="R_HMR_4356" metaid="e6efa094-5aeb-412c-8390-f6707d0794e0" name="R_HMR_4356" reversible="false" sboTerm="SBO:0000176">\r\n+ <notes>\r\n+ <body xmlns="http://www.w3.org/1999/xhtml">\r\n+ Confidence Level: 0\r\n+ AUTHORS: PMID:5114731;PMID:5655259;PMID:6054986\r\n+ ec-code: 4.1.2.13\r\n+ metanetx.reaction: MNXR99460\r\n+ kegg.reaction: R02568\r\n+ bigg.reaction: FBA2\r\n+ SUBSYSTEM: Fructose and mannose metabolism\r\n+ EC_NUMBER: 4.1.2.13\r\n+ pmids: 5114731,5655259,6054986\r\n+ GENE_ASSOCIATION: ( ENSG00000109107 ) OR ( ENSG00000136872 ) OR ( ENSG00000149925 ) OR ( ENSG00000285043 )\r\n+ </body>\r\n+ </notes>\r\n+ <annotation>\r\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\r\n+ <rdf:Description rdf:about="#e6efa094-5aeb-412c-8390-f6707d0794e0">\r\n+ <bqbiol:is>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/ec-code/4.1.2.13"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR99460"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/kegg.reaction/R02568"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FBA2"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:is>\r\n+ <bqbiol:isDescribedBy>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/pubmed/5114731"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/pubmed/6054986"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/pubmed/5655259"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:isDescribedBy>\r\n+ </rdf:Description>\r\n+ </rdf:RDF>\r\n+ </annotation>\r\n+ <fbc:geneProductAssociation>\r\n+ <fbc:or>\r\n+ <fbc:geneProductRef fbc:geneProduct="ENSG00000136872"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="ENSG00000149925"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="ENSG00000109107"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="ENSG00000285043"/>\r\n+ </fbc:or>\r\n+ </fbc:geneProductAssociation>\r\n+ <listOfReactants>\r\n+ <speciesReference constant="true" species="M_m01690c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_m01981c" stoichiometry="1"/>\r\n+ </listOfReactants>\r\n+ <listOfProducts>\r\n+ <speciesReference constant="true" species="M_m01842c" stoichiometry="1"/>\r\n+ </listOfProducts>\r\n+ </reaction>\r\n+ </listOfReactions>\r\n+ </model>\r\n+</sbml>\r\n'

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/ExtractPathways/ExtractPathways.xml
--- a/tools/attributes/ExtractPathways/ExtractPathways.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/ExtractPathways/ExtractPathways.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractPathways" name="ExtractPathways" version="1.0.1">
+<tool id="met4j_ExtractPathways" name="ExtractPathways" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath"
 -p "$pathwayId"

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml
--- a/tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="1.0.1">
+<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractSbmlAnnot -i "$inputPath"
 -export "$export"

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.1.0">
+ <description>Get gene lists from a list of reactions and a GSMN.</description>
+ <xrefs>
+ <xref type="bio.tools">met4j</xref>
+ </xrefs>
+ <requirements>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ </requirements>
+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
+ -r "$reactionFile"
+#if str($sep):
+ -sep "$sep"
+#end if
+ $hasHeader
+#if str($i) != 'nan':
+ -col "$i"
+#end if
+ -o "$outputFile"
+]]></command>
+ <inputs>
+ <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
+ <param argument="-r" format="tsv" label="Input Reaction file" name="reactionFile" optional="false" type="data" value=""/>
+ <param argument="-sep" label="Separator in reaction file" name="sep" optional="true" type="text" value="	">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ <param argument="-header" checked="false" falsevalue="" label="Skip reaction file header" name="hasHeader" truevalue="-header" type="boolean" value="false"/>
+ <param argument="-col" label="Column number in reaction file (first as 1)" name="i" optional="true" type="integer" value="1"/>
+ </inputs>
+ <outputs>
+ <data format="tsv" name="outputFile"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="sbml" value="XF_network.sbml"/>
+ <param name="reactionFile" value="XF_network_R_Seed.tab"/>
+ <output ftype="tsv" name="outputFile">
+ <assert_contents>
+ <has_n_lines n="2"/>
+ <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
+ <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
+ </assert_contents>
+ </output>
+ </test>
+ </tests>
+ <help><![CDATA[Get associated gene list from a list of reactions and a GSMN. Parse GSMN GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
+ <citations/>
+</tool>

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/GetGenesFromReactions/test-data/XF_network.sbml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/GetGenesFromReactions/test-data/XF_network.sbml Fri Jul 29 13:23:40 2022 +0000

b'@@ -0,0 +1,47267 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<sbml fbc:required="false" groups:required="false" level="3" version="2" xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1">\n+ <model fbc:strict="true" id="Xfm1158" metaid="Xfm1158" name="Xfm1158">\n+ <fbc:listOfGeneProducts>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_007090" fbc:label="XFCFBP8418_007090" fbc:name="XFCFBP8418_007090" metaid="_8a7d7180-d79e-4dbb-86ed-f8d7eb60e698"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_005900" fbc:label="XFCFBP8418_005900" fbc:name="XFCFBP8418_005900" metaid="_867487dd-ff57-4e93-8de9-b5ecb805e0eb"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_011590" fbc:label="XFCFBP8418_011590" fbc:name="XFCFBP8418_011590" metaid="_44606760-936c-4585-b40c-650e953a5f73"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_014620" fbc:label="XFCFBP8418_014620" fbc:name="XFCFBP8418_014620" metaid="da273da9-0f84-4615-a464-2ab71416e8cc"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_015830" fbc:label="XFCFBP8418_015830" fbc:name="XFCFBP8418_015830" metaid="_3a9239a2-8e23-4834-99a8-a7dc15f6d906"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_014980" fbc:label="XFCFBP8418_014980" fbc:name="XFCFBP8418_014980" metaid="_7f26806b-e32e-4c5c-a78d-9e094c267bbf"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_020190" fbc:label="XFCFBP8418_020190" fbc:name="XFCFBP8418_020190" metaid="_31bbb514-1d52-4727-91cb-367af12e95ca"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_004940" fbc:label="XFCFBP8418_004940" fbc:name="XFCFBP8418_004940" metaid="a2f20753-c245-477e-8363-8f5e45c50f5d"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_021160" fbc:label="XFCFBP8418_021160" fbc:name="XFCFBP8418_021160" metaid="_844bdacc-d091-457d-9c4d-846cb9aab3c1"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_025760" fbc:label="XFCFBP8418_025760" fbc:name="XFCFBP8418_025760" metaid="fd8a601e-e56f-4263-9aa7-6ed9bf85f958"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_024670" fbc:label="XFCFBP8418_024670" fbc:name="XFCFBP8418_024670" metaid="_2bbe03ce-c814-417a-b9c0-e8a1f29f4106"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_004820" fbc:label="XFCFBP8418_004820" fbc:name="XFCFBP8418_004820" metaid="_41cb6d94-13d8-461e-a217-29a68e21cd2b"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_023580" fbc:label="XFCFBP8418_023580" fbc:name="XFCFBP8418_023580" metaid="_31ff72d7-4e30-4563-85aa-4afc58dd6bee"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_000460" fbc:label="XFCFBP8418_000460" fbc:name="XFCFBP8418_000460" metaid="d7ea14e6-cd6c-4404-b973-486ade662242"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_026730" fbc:label="XFCFBP8418_026730" fbc:name="XFCFBP8418_026730" metaid="e876348e-787e-4f2a-8904-e675c2589c17"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_025640" fbc:label="XFCFBP8418_025640" fbc:name="XFCFBP8418_025640" metaid="b5b93812-bd2e-4ca8-8328-e1d35e17ac3a"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_023100" fbc:label="XFCFBP8418_023100" fbc:name="XFCFBP8418_023100" metaid="f62e0096-7b12-4db3-a7b0-2e1cfa0302c6"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_027800" fbc:label="XFCFBP8418_027800" fbc:name="XFCFBP8418_027800" metaid="_8beb93ba-34a4-4330-86bf-2c47b1cb7f2e"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_004700" fbc:label="XFCFBP8418_004700" fbc:name="XFCFBP8418_004700" metaid="_2aceabe8-5294-42eb-9d3b-2506634c68d5"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_005910" fbc:label="XFCFBP8418_005910" fbc:name="XFCFBP8418_005910" metaid="a7b44241-024e-49c1-88af-1e1108cf09eb"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_013540" fbc:label="XFCFBP8418_013540" fbc:name="XFCFBP8418_013540" metaid="_83bdba7b-0eb0-4dfb-99ed-6e365240d870"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_011240" fbc:label="XFCFBP8418_011240" fbc:name="XFCFBP8418_011240" metaid="_568b9959-99b6-49bd-86d7-04e773d940da"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_012210" fbc:label="XFCFBP8418_01221'..b' </annotation>\n+ <fbc:geneProductAssociation>\n+ <fbc:geneProductRef fbc:geneProduct="XFCFBP8418_010590"/>\n+ </fbc:geneProductAssociation>\n+ <listOfReactants>\n+ <speciesReference constant="true" species="M_cyst_L_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference constant="true" species="M_2obut_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_cys_L_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1"/>\n+ </listOfProducts>\n+ </reaction>\n+ <reaction fbc:lowerFluxBound="LOWER_BOUND_99999_0" fbc:upperFluxBound="UPPER_BOUND_99999_0" id="R_FUCtpp" metaid="_34363cfc-fa7f-4df4-a073-49f5befcdf50" name="R_FUCtpp" reversible="true">\n+ <notes>\n+ <body xmlns="http://www.w3.org/1999/xhtml">\n+ GENE_ASSOCIATION: XFCFBP8418_018650\n+ SUBSYSTEM: Transport__Inner_Membrane\n+ EC_NUMBER: No_Assignment\n+ </body>\n+ </notes>\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_34363cfc-fa7f-4df4-a073-49f5befcdf50">\n+ <bqbiol:is>\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/ec-code/No_Assignment"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </annotation>\n+ <fbc:geneProductAssociation>\n+ <fbc:geneProductRef fbc:geneProduct="XFCFBP8418_018650"/>\n+ </fbc:geneProductAssociation>\n+ <listOfReactants>\n+ <speciesReference constant="true" species="M_h_p" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_fuc_L_p" stoichiometry="1"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference constant="true" species="M_fuc_L_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_h_c" stoichiometry="1"/>\n+ </listOfProducts>\n+ </reaction>\n+ <reaction fbc:lowerFluxBound="LOWER_BOUND_0_0" fbc:upperFluxBound="UPPER_BOUND_99999_0" id="R_FACOAE120" metaid="_2691931b-9cfe-40d9-95d9-13e4ed057413" name="R_FACOAE120" reversible="false">\n+ <notes>\n+ <body xmlns="http://www.w3.org/1999/xhtml">\n+ GENE_ASSOCIATION: XFCFBP8418_025070\n+ SUBSYSTEM: Cell_Envelope_Biosynthesis\n+ EC_NUMBER: 3.1.2.20\n+ </body>\n+ </notes>\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2691931b-9cfe-40d9-95d9-13e4ed057413">\n+ <bqbiol:is>\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.20"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </annotation>\n+ <fbc:geneProductAssociation>\n+ <fbc:geneProductRef fbc:geneProduct="XFCFBP8418_025070"/>\n+ </fbc:geneProductAssociation>\n+ <listOfReactants>\n+ <speciesReference constant="true" species="M_ddcacoa_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_h_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>\n+ </listOfProducts>\n+ </reaction>\n+ </listOfReactions>\n+ </model>\n+</sbml>\n'

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/GetGenesFromReactions/test-data/XF_network_R_Seed.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/GetGenesFromReactions/test-data/XF_network_R_Seed.tab Fri Jul 29 13:23:40 2022 +0000

@@ -0,0 +1,2 @@
+R_ACGS
+R_GLUN

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -0,0 +1,75 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="1.1.0">
+ <description>Get reactants lists from a list of reactions and a GSMN.</description>
+ <xrefs>
+ <xref type="bio.tools">met4j</xref>
+ </xrefs>
+ <requirements>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ </requirements>
+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetReactantsFromReactions -i "$sbml"
+ -r "$reactionFile"
+#if str($sep):
+ -sep "$sep"
+#end if
+ $hasHeader
+#if str($i) != 'nan':
+ -col "$i"
+#end if
+ $printSubstrates
+ $printProducts
+ -o "$outputFile"
+]]></command>
+ <inputs>
+ <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
+ <param argument="-r" format="tsv" label="Input Reaction file" name="reactionFile" optional="false" type="data" value=""/>
+ <param argument="-sep" label="Separator in reaction file" name="sep" optional="true" type="text" value="	">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ <param argument="-header" checked="false" falsevalue="" label="Skip reaction file header" name="hasHeader" truevalue="-header" type="boolean" value="false"/>
+ <param argument="-col" label="Column number in reaction file (first as 1)" name="i" optional="true" type="integer" value="1"/>
+ <param argument="-s" checked="false" falsevalue="" label="Extract substrates only" name="printSubstrates" truevalue="-s" type="boolean" value="false"/>
+ <param argument="-p" checked="false" falsevalue="" label="Extract products only" name="printProducts" truevalue="-p" type="boolean" value="false"/>
+ </inputs>
+ <outputs>
+ <data format="tsv" name="outputFile"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="sbml" value="XF_network.sbml"/>
+ <param name="reactionFile" value="XF_network_R_Seed.tab"/>
+ <output ftype="tsv" name="outputFile">
+ <assert_contents>
+ <has_text_matching expression="R_GLUN" n="4"/>
+ <has_text_matching expression="R_ACGS" n="5"/>
+ </assert_contents>
+ </output>
+ </test>
+ <test>
+ <param name="sbml" value="XF_network.sbml"/>
+ <param name="reactionFile" value="XF_network_R_Seed.tab"/>
+ <param name="printSubstrates" value="true"/>
+ <output ftype="tsv" name="outputFile">
+ <assert_contents>
+ <has_text_matching expression="R_GLUN" n="2"/>
+ <has_text_matching expression="R_ACGS" n="5"/>
+ </assert_contents>
+ </output>
+ </test>
+ <test>
+ <param name="sbml" value="XF_network.sbml"/>
+ <param name="reactionFile" value="XF_network_R_Seed.tab"/>
+ <param name="printProducts" value="true"/>
+ <output ftype="tsv" name="outputFile">
+ <assert_contents>
+ <has_text_matching expression="R_GLUN" n="2"/>
+ <has_text_matching expression="R_ACGS" n="5"/>
+ </assert_contents>
+ </output>
+ </test>
+ </tests>
+ <help><![CDATA[Get reactants lists from a list of reactions and a GSMN. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered both substrates and products]]></help>
+ <citations/>
+</tool>

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/GetReactantsFromReactions/test-data/XF_network.sbml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/GetReactantsFromReactions/test-data/XF_network.sbml Fri Jul 29 13:23:40 2022 +0000

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/GetReactantsFromReactions/test-data/XF_network_R_Seed.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/GetReactantsFromReactions/test-data/XF_network_R_Seed.tab Fri Jul 29 13:23:40 2022 +0000

@@ -0,0 +1,2 @@
+R_ACGS
+R_GLUN

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml
--- a/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.0.1">
+<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan':
 -cc "$colcharge"

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml
--- a/tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="1.0.1">
+<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetEcsFromFile#if str($colec) != 'nan':
 -cec "$colec"

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml
--- a/tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="1.0.1">
+<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan':
 -cf "$colformula"

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml
--- a/tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="1.0.1">
+<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan':
 -cgpr "$colgpr"

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml
--- a/tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="1.0.1">
+<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetNamesFromFile#if str($colname) != 'nan':
 -cname "$colname"

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml
--- a/tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.0.1">
+<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan':
 -cp "$colp"

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml
--- a/tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.0.1">
+<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan':
 -cr "$colRef"

diff -r e69a78624877 -r 6bd9aad9626d tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml
--- a/tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="1.0.1">
+<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlToMetaboliteTable -s "$sbml"
 -o "$outputFile"

diff -r e69a78624877 -r 6bd9aad9626d tools/bigg/GetModelProteome/GetModelProteome.xml
--- a/tools/bigg/GetModelProteome/GetModelProteome.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/bigg/GetModelProteome/GetModelProteome.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_GetModelProteome" name="GetModelProteome" version="1.0.1">
+<tool id="met4j_GetModelProteome" name="GetModelProteome" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetModelProteome -m "$modelId"
 -o "$outputFile"

diff -r e69a78624877 -r 6bd9aad9626d tools/convert/FbcToNotes/FbcToNotes.xml
--- a/tools/convert/FbcToNotes/FbcToNotes.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/convert/FbcToNotes/FbcToNotes.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_FbcToNotes" name="FbcToNotes" version="1.0.1">
+<tool id="met4j_FbcToNotes" name="FbcToNotes" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath"
 -o "$outputPath"

diff -r e69a78624877 -r 6bd9aad9626d tools/convert/Kegg2Sbml/Kegg2Sbml.xml
--- a/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="1.0.1">
+<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org):
 -org "$org"

diff -r e69a78624877 -r 6bd9aad9626d tools/convert/Sbml2Graph/Sbml2Graph.xml
--- a/tools/convert/Sbml2Graph/Sbml2Graph.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/convert/Sbml2Graph/Sbml2Graph.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.0.1">
+<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
 $bipartite

diff -r e69a78624877 -r 6bd9aad9626d tools/convert/Sbml2Tab/Sbml2Tab.xml
--- a/tools/convert/Sbml2Tab/Sbml2Tab.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/convert/Sbml2Tab/Sbml2Tab.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="1.0.1">
+<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i):
 -i "$i"

diff -r e69a78624877 -r 6bd9aad9626d tools/convert/Tab2Sbml/Tab2Sbml.xml
--- a/tools/convert/Tab2Sbml/Tab2Sbml.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/convert/Tab2Sbml/Tab2Sbml.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.0.1">
+<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan':
 -ci "$colid"

diff -r e69a78624877 -r 6bd9aad9626d tools/met4j.yml
--- a/tools/met4j.yml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/met4j.yml Fri Jul 29 13:23:40 2022 +0000

@@ -3,12 +3,21 @@
install_resolver_dependencies: true
install_tool_dependencies: false
tools:
+  - name: DecomposeSBML
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
   - name: ExtractPathways
     owner: metexplore
     tool_panel_section_id: met4j_attributes
   - name: ExtractSbmlAnnot
     owner: metexplore
     tool_panel_section_id: met4j_attributes
+  - name: GetGenesFromReactions
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
+  - name: GetReactantsFromReactions
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
   - name: SbmlSetChargesFromFile
     owner: metexplore
     tool_panel_section_id: met4j_attributes

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml
--- a/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.0.1">
+<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath"
 -g "$inputAAM"

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/ChokePoint/ChokePoint.xml
--- a/tools/networkAnalysis/ChokePoint/ChokePoint.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/ChokePoint/ChokePoint.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ChokePoint" name="ChokePoint" version="1.0.1">
+<tool id="met4j_ChokePoint" name="ChokePoint" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
#if str($sideCompoundFile) != 'None':

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/CompoundNet/CompoundNet.xml
--- a/tools/networkAnalysis/CompoundNet/CompoundNet.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/CompoundNet/CompoundNet.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_CompoundNet" name="CompoundNet" version="1.0.1">
+<tool id="met4j_CompoundNet" name="CompoundNet" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath"
#if str($inputSide) != 'None':

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml
--- a/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="1.0.1">
+<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
#if str($sideCompoundFile) != 'None':

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml
--- a/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="1.0.1">
+<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath"
 -s "$sourcePath"

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml
--- a/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="1.0.1">
+<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath"
 -s "$sourcePath"

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml
--- a/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.0.1">
+<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
 -s "$sourcePath"

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/LoadPoint/LoadPoint.xml
--- a/tools/networkAnalysis/LoadPoint/LoadPoint.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/LoadPoint/LoadPoint.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_LoadPoint" name="LoadPoint" version="1.0.1">
+<tool id="met4j_LoadPoint" name="LoadPoint" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath"
#if str($sideCompoundFile) != 'None':

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/MetaboRank/MetaboRank.xml
--- a/tools/networkAnalysis/MetaboRank/MetaboRank.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/MetaboRank/MetaboRank.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_MetaboRank" name="MetaboRank" version="1.0.1">
+<tool id="met4j_MetaboRank" name="MetaboRank" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath"
 -s "$seedsFilePath"

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/NetworkSummary/NetworkSummary.xml
--- a/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.0.1">
+<tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath"
#if str($sideCompoundFile) != 'None':

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml
--- a/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.0.1">
+<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath"
 -t "$targetsFilePath"

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml
--- a/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.0.1">
+<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
 -s "$seedsFilePath"

diff -r e69a78624877 -r 6bd9aad9626d tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml
--- a/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml Fri Jul 29 13:23:40 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="1.0.1">
+<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="1.1.0">
 <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:1.0.1</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath"
 $sideOnly

diff -r e69a78624877 -r 6bd9aad9626d tools/tool_conf.xml
--- a/tools/tool_conf.xml Tue Jul 19 14:20:07 2022 +0000
+++ b/tools/tool_conf.xml Fri Jul 29 13:23:40 2022 +0000

@@ -2,8 +2,11 @@
<toolbox monitor="true">
 <label id="met4j" text="MET4J"/>
 <section id="met4j_attributes" name="Met4J - attributes"/>
+ <tool file="met4j/attributes/DecomposeSBML/DecomposeSBML.xml"/>
 <tool file="met4j/attributes/ExtractPathways/ExtractPathways.xml"/>
 <tool file="met4j/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml"/>
+ <tool file="met4j/attributes/GetGenesFromReactions/GetGenesFromReactions.xml"/>
+ <tool file="met4j/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml"/>
 <tool file="met4j/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml"/>
 <tool file="met4j/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml"/>
 <tool file="met4j/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml"/>