# HG changeset patch # User metexplore # Date 1738598386 0 # Node ID 6a112eaf8f3890a357a5abcc934716c86062ed1b # Parent 0976a62573004788d3ee3963192d8e974fcc6445 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95 diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml --- a/build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Create a compound to reactions distance matrix. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Compute the Choke points of a metabolic network. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a Meta-Network from two sub-networks in SBML format. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Provides tabulated compound graph edge list, with one column with target's degree. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Create a compound to compound distance matrix. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Extract databases' references from SBML annotations or notes. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/ExtractPathways/ExtractPathways.xml --- a/build/tools/ExtractPathways/ExtractPathways.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/ExtractPathways/ExtractPathways.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Extract pathway(s) from a SBML file and create a sub-network SBML file met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml --- a/build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Create a subnetwork from a metabolic network 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. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10.1093/bib/bbv115 diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml --- a/build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Create a subnetwork from a metabolic network 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. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Convert FBC package annotations to sbml html notes met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/GetBiggModelProteome/GetBiggModelProteome.xml --- a/build/tools/GetBiggModelProteome/GetBiggModelProteome.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/GetBiggModelProteome/GetBiggModelProteome.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Get proteome in fasta format of a model present in the BIGG database met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/GetEntities/GetEntities.xml --- a/build/tools/GetEntities/GetEntities.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/GetEntities/GetEntities.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/GetGenesFromReactions/GetGenesFromReactions.xml --- a/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Get gene lists from a list of reactions and a SBML file. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.xml --- a/build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Create a tabulated file with metabolite attributes from a SBML file met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml --- a/build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Get reactant lists from a list of reactions and a SBML file. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/Kegg2Sbml/Kegg2Sbml.xml --- a/build/tools/Kegg2Sbml/Kegg2Sbml.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/Kegg2Sbml/Kegg2Sbml.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Build a SBML file from KEGG organism-specific pathways. Uses Kegg API. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Compute the MetaboRank, a custom personalized PageRank for metabolic network. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + This tool runs edit-distance based fuzzy matching to perform near-similar name matching between a metabolic model and a list of chemical names in a dataset. A harmonization processing is performed on chemical names with substitutions of common patterns among synonyms, in order to create aliases on which classical fuzzy matching can be run efficiently. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/NetworkSummary/NetworkSummary.xml --- a/build/tools/NetworkSummary/NetworkSummary.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/NetworkSummary/NetworkSummary.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Create a report summarizing several graph measures characterising the structure of a metabolic network. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Perform a network expansion from a set of compound targets to create a precursor network. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a reaction to reaction distance matrix. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam) met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml --- a/build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Advanced creation of a compound graph representation of a SBML file content met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a graph representation of a SBML file content, and export it in graph file format. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Creation of a Pathway Network representation of a SBML file content met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Create a tabulated file listing reaction attributes from a SBML file met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/SbmlCheckBalance/SbmlCheckBalance.xml --- a/build/tools/SbmlCheckBalance/SbmlCheckBalance.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/SbmlCheckBalance/SbmlCheckBalance.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Check balance of all the reactions in a SBML. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + General SBML model processing met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/ScopeNetwork/ScopeNetwork.xml --- a/build/tools/ScopeNetwork/ScopeNetwork.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/ScopeNetwork/ScopeNetwork.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Perform a network expansion from a set of compound seeds to create a scope network met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + 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 met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set names to network objects in a SBML file from a tabulated file containing the object ids and the names met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Scan a network to identify side compounds. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a Sbml File from a tabulated file that contains the reaction ids and the formulas met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml --- a/build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff -r 0976a6257300 -r 6a112eaf8f38 tools/attributes/ExtractAnnotations/ExtractAnnotations.xml --- a/tools/attributes/ExtractAnnotations/ExtractAnnotations.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/ExtractAnnotations/ExtractAnnotations.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Extract databases' references from SBML annotations or notes. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/attributes/ExtractPathways/ExtractPathways.xml --- a/tools/attributes/ExtractPathways/ExtractPathways.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/ExtractPathways/ExtractPathways.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Extract pathway(s) from a SBML file and create a sub-network SBML file met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/attributes/GetEntities/GetEntities.xml --- a/tools/attributes/GetEntities/GetEntities.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/GetEntities/GetEntities.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml --- a/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Get gene lists from a list of reactions and a SBML file. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml --- a/tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Create a tabulated file with metabolite attributes from a SBML file met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml --- a/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Get reactant lists from a list of reactions and a SBML file. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/attributes/SetCharges/SetCharges.xml --- a/tools/attributes/SetCharges/SetCharges.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/SetCharges/SetCharges.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + 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 met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set names to network objects in a SBML file from a tabulated file containing the object ids and the names met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Get proteome in fasta format of a model present in the BIGG database met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/convert/FbcToNotes/FbcToNotes.xml --- a/tools/convert/FbcToNotes/FbcToNotes.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/convert/FbcToNotes/FbcToNotes.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Convert FBC package annotations to sbml html notes met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/convert/Kegg2Sbml/Kegg2Sbml.xml --- a/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Build a SBML file from KEGG organism-specific pathways. Uses Kegg API. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam) met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml --- a/tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Advanced creation of a compound graph representation of a SBML file content met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a graph representation of a SBML file content, and export it in graph file format. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Creation of a Pathway Network representation of a SBML file content met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Create a tabulated file listing reaction attributes from a SBML file met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/convert/SbmlWizard/SbmlWizard.xml --- a/tools/convert/SbmlWizard/SbmlWizard.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/convert/SbmlWizard/SbmlWizard.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + General SBML model processing met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/convert/Tab2Sbml/Tab2Sbml.xml --- a/tools/convert/Tab2Sbml/Tab2Sbml.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/convert/Tab2Sbml/Tab2Sbml.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Create a Sbml File from a tabulated file that contains the reaction ids and the formulas met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 0976a6257300 -r 6a112eaf8f38 tools/mapping/NameMatcher/NameMatcher.xml --- a/tools/mapping/NameMatcher/NameMatcher.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/mapping/NameMatcher/NameMatcher.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + This tool runs edit-distance based fuzzy matching to perform near-similar name matching between a metabolic model and a list of chemical names in a dataset. A harmonization processing is performed on chemical names with substitutions of common patterns among synonyms, in order to create aliases on which classical fuzzy matching can be run efficiently. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 diff -r 0976a6257300 -r 6a112eaf8f38 tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml --- a/tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a compound to reactions distance matrix. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Compute the Choke points of a metabolic network. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Provides tabulated compound graph edge list, with one column with target's degree. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - + Create a compound to compound distance matrix. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a subnetwork from a metabolic network 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. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10.1093/bib/bbv115 diff -r 0976a6257300 -r 6a112eaf8f38 tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml --- a/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ - + Create a subnetwork from a metabolic network 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. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Compute the MetaboRank, a custom personalized PageRank for metabolic network. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a report summarizing several graph measures characterising the structure of a metabolic network. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Perform a network expansion from a set of compound targets to create a precursor network. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a reaction to reaction distance matrix. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Perform a network expansion from a set of compound seeds to create a scope network met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Scan a network to identify side compounds. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a Meta-Network from two sub-networks in SBML format. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Check balance of all the reactions in a SBML. met4j - oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop + oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0