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Commit message:
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5 |
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modified:
HowTo.md build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml build/tools/CarbonSkeletonNet/CarbonSkeletonNet.xml build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml build/tools/ChokePoint/ChokePoint.xml build/tools/CompoundNet/CompoundNet.xml build/tools/DecomposeSBML/DecomposeSBML.xml build/tools/DegreeWeighting/DegreeWeighting.xml build/tools/DistanceMatrix/DistanceMatrix.xml build/tools/ExtractPathways/ExtractPathways.xml build/tools/ExtractSbmlAnnot/ExtractSbmlAnnot.xml build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml build/tools/ExtractSubNetwork/ExtractSubNetwork.xml build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml build/tools/FbcToNotes/FbcToNotes.xml build/tools/GetGenesFromReactions/GetGenesFromReactions.xml build/tools/GetModelProteome/GetModelProteome.xml build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml build/tools/Kegg2Sbml/Kegg2Sbml.xml build/tools/LoadPoint/LoadPoint.xml build/tools/MetaboRank/MetaboRank.xml build/tools/NameMatcher/NameMatcher.xml build/tools/NetworkSummary/NetworkSummary.xml build/tools/PathwayNet/PathwayNet.xml build/tools/PrecursorNetwork/PrecursorNetwork.xml build/tools/Sbml2Graph/Sbml2Graph.xml build/tools/Sbml2Tab/Sbml2Tab.xml build/tools/SbmlCheckBalance/SbmlCheckBalance.xml build/tools/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml build/tools/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml build/tools/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml build/tools/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml build/tools/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml build/tools/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml build/tools/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml build/tools/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml build/tools/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml build/tools/ScopeNetwork/ScopeNetwork.xml build/tools/SeedsAndTargets/SeedsAndTargets.xml build/tools/SideCompoundsScan/SideCompoundsScan.xml build/tools/Tab2Sbml/Tab2Sbml.xml tests.html tools/met4j.yml tools/networkAnalysis/ChokePoint/ChokePoint.xml tools/networkAnalysis/MetaboRank/MetaboRank.xml tools/tool_conf.xml |
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added:
build/tools/MetaboRank/test-data/XF_network.sbml build/tools/MetaboRank/test-data/XF_network_C_Seed.tab build/tools/MetaboRank/test-data/XF_network_C_Side.tab build/tools/SBMLwizard/SBMLwizard.xml build/tools/SBMLwizard/test-data/Human-GEM_pathways.xml build/tools/SBMLwizard/test-data/XF_network.sbml build/tools/SBMLwizard/test-data/XF_network_C_Side.tab build/tools/SBMLwizard/test-data/XF_network_R_Seed.tab data/XF_network_C_Seed.tab tools/convert/SBMLwizard/SBMLwizard.xml tools/convert/SBMLwizard/test-data/Human-GEM_pathways.xml tools/convert/SBMLwizard/test-data/XF_network.sbml tools/convert/SBMLwizard/test-data/XF_network_C_Side.tab tools/convert/SBMLwizard/test-data/XF_network_R_Seed.tab tools/networkAnalysis/MetaboRank/test-data/XF_network.sbml tools/networkAnalysis/MetaboRank/test-data/XF_network_C_Seed.tab tools/networkAnalysis/MetaboRank/test-data/XF_network_C_Side.tab |
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removed:
build/tools/ChokePoint/test-data/sides.txt build/tools/MetaboRank/test-data/edgeWeights.tsv build/tools/MetaboRank/test-data/toy_model.xml build/tools/MetaboRank/test-data/weights.txt tools/networkAnalysis/ChokePoint/test-data/sides.txt tools/networkAnalysis/MetaboRank/test-data/edgeWeights.tsv tools/networkAnalysis/MetaboRank/test-data/toy_model.xml tools/networkAnalysis/MetaboRank/test-data/weights.txt |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 HowTo.md --- a/HowTo.md Wed May 17 13:26:37 2023 +0000 +++ b/HowTo.md Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -94,7 +94,17 @@ When tests are ok, you can create a new met4j release. The CI will create a new Singularity image corresponding to this version. -Create a new met4j-galaxy release with the same version number as met4j. After push, the CI will test again the apps. If it's ok, a new version of met4j-galaxy will be pushed on the galaxy toolshed. The instance in usegalaxy.fr will be updated the next monday. +Create a new met4j-galaxy release with the same version number as met4j. + +After testing this new version, you have to do: + +```bash +git push origin 1.3.0 +``` + +Modify the 1.3.0 by the version number that you want to push. + +After push, the CI will test again the apps. If it's ok, a new version of met4j-galaxy will be pushed on the galaxy toolshed. The instance in usegalaxy.fr will be updated the next monday. ## Update met4j-galaxy-runner |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml --- a/build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="1.3.0"> +<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="1.4.0"> <description>Create a compound to reactions distance matrix.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.BipartiteDistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/CarbonSkeletonNet/CarbonSkeletonNet.xml --- a/build/tools/CarbonSkeletonNet/CarbonSkeletonNet.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/CarbonSkeletonNet/CarbonSkeletonNet.xml Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.3.0"> +<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.4.0"> <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:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath" -g "$inputAAM" |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml --- a/build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.3.0"> +<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.4.0"> <description>Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type): -f "$type" |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/ChokePoint/ChokePoint.xml --- a/build/tools/ChokePoint/ChokePoint.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/ChokePoint/ChokePoint.xml Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -1,21 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ChokePoint" name="ChokePoint" version="1.3.0"> +<tool id="met4j_ChokePoint" name="ChokePoint" version="1.4.0"> <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:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath" -#if str($sideCompoundFile) != 'None': - -s "$sideCompoundFile" -#end if -o "$outputPath" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/> </inputs> <outputs> <data format="tsv" name="outputPath"/> @@ -25,28 +21,16 @@ <param name="inputPath" value="XF_network.sbml"/> <output ftype="tsv" name="outputPath"> <assert_contents> - <has_n_lines n="202"/> + <has_n_lines n="695"/> <has_n_columns n="3"/> <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e <==> M_ade_p" n="1"/> - <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --> M_ru5p_L_c" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="XF_network.sbml"/> - <param name="sideCompoundFile" value="sides.txt"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="200"/> - <has_n_columns n="3"/> - <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e <==> M_ade_p" n="1" negate="true"/> - <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --> M_ru5p_L_c" n="1" negate="true"/> + <has_line_matching expression="R_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --> M_ac_c \+ M_gam6p_c" n="1"/> </assert_contents> </output> </test> </tests> <help><![CDATA[Compute the Choke points of a metabolic network. -Load points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target +Choke points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target See : Syed Asad Rahman, Dietmar Schomburg; Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinformatics 2006; 22 (14): 1767-1774. doi: 10.1093/bioinformatics/btl181]]></help> <citations/> </tool> |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/ChokePoint/test-data/sides.txt --- a/build/tools/ChokePoint/test-data/sides.txt Wed May 17 13:26:37 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -M_xu5p_L_c -M_ru5p_L_c -M_ade_e -M_ade_p \ No newline at end of file |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/CompoundNet/CompoundNet.xml --- a/build/tools/CompoundNet/CompoundNet.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/CompoundNet/CompoundNet.xml Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_CompoundNet" name="CompoundNet" version="1.3.0"> +<tool id="met4j_CompoundNet" name="CompoundNet" version="1.4.0"> <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:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/MetaboRank/test-data/weights.txt --- a/build/tools/MetaboRank/test-data/weights.txt Wed May 17 13:26:37 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -B 10 -C 1 \ No newline at end of file |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/NameMatcher/NameMatcher.xml --- a/build/tools/NameMatcher/NameMatcher.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/NameMatcher/NameMatcher.xml Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_NameMatcher" name="NameMatcher" version="1.3.0"> +<tool id="met4j_NameMatcher" name="NameMatcher" version="1.4.0"> <description>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.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.NameMatcher#if str($n): -nMatch "$n" |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/NetworkSummary/NetworkSummary.xml --- a/build/tools/NetworkSummary/NetworkSummary.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/NetworkSummary/NetworkSummary.xml Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.3.0"> +<tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.4.0"> <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:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath" #if str($sideCompoundFile) != 'None': |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/PathwayNet/PathwayNet.xml --- a/build/tools/PathwayNet/PathwayNet.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/PathwayNet/PathwayNet.xml Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_PathwayNet" name="PathwayNet" version="1.3.0"> +<tool id="met4j_PathwayNet" name="PathwayNet" version="1.4.0"> <description>Creation of a Pathway Network 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:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PathwayNet -s "$inputPath" #if str($inputSide) != 'None': |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/PrecursorNetwork/PrecursorNetwork.xml --- a/build/tools/PrecursorNetwork/PrecursorNetwork.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/PrecursorNetwork/PrecursorNetwork.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.3.0"> +<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.4.0"> <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:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" -t "$targetsFilePath" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SBMLwizard/SBMLwizard.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SBMLwizard/SBMLwizard.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -0,0 +1,79 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="met4j_SBMLwizard" name="SBMLwizard" version="1.4.0"> + <description>General SBML model processing</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SBMLwizard -s "$inputPath" +#if str($inputSide) != 'None': + -rc "$inputSide" +#end if + $removeIsolated +#if str($inputReactions) != 'None': + -rr "$inputReactions" +#end if + $removeNoFlux +#if str($mergingStrat): + -mc "$mergingStrat" +#end if + $removeDuplicated +#if str($exchangeCompToRemove): + -rEX "$exchangeCompToRemove" +#end if + -o "$outputPath" +]]></command> + <inputs> + <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-rc" format="txt" label="file containing identifiers of compounds to remove from the metabolic network" name="inputSide" optional="true" type="data" value=""/> + <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/> + <param argument="-rr" format="txt" label="file containing identifiers of reactions to remove from the metabolic network" name="inputReactions" optional="true" type="data" value=""/> + <param argument="-r0" checked="false" falsevalue="" label="remove reactions with lower and upper flux bounds both set to 0.0" name="removeNoFlux" truevalue="-r0" type="boolean" value="false"/> + <param argument="-mc" label="merge compartments using the provided strategy. No merge by default. "by_name" can be used if names are consistent and unambiguous across compartments, "by_id" can be used if compartment suffix is present in compounds identifiers (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no"> + <option selected="true" value="no">no</option> + <option value="by_name">by_name</option> + <option value="by_id">by_id</option> + </param> + <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/> + <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="outputPath"/> + </outputs> + <tests> + <test> + <param name="inputPath" value="Human-GEM_pathways.xml"/> + <param name="removeIsolated" value="true"/> + <param name="removeNoFlux" value="true"/> + <param name="mergingStrat" value="by_id"/> + <param name="removeDuplicated" value="true"/> + <param name="exchangeCompToRemove" value="s"/> + <output ftype="sbml" name="outputPath"> + <assert_contents> + <has_text text="</sbml>"/> + </assert_contents> + </output> + </test> + <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="removeIsolated" value="true"/> + <param name="removeNoFlux" value="true"/> + <param name="removeDuplicated" value="true"/> + <param name="inputSide" value="XF_network_C_Side.tab"/> + <param name="inputReactions" value="XF_network_R_Seed.tab"/> + <output ftype="sbml" name="outputPath"> + <assert_contents> + <has_text text="</sbml>"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help> + <citations/> +</tool> |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SBMLwizard/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SBMLwizard/test-data/Human-GEM_pathways.xml Tue Jul 04 10:21:26 2023 +0000 |
| b |
| 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+ <p>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.</p>\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+ <p>ensembl: ENSG00000023697</p>\r\n+ <p>hgnc.symbol: DERA</p>\r\n+ <p>ncbigene: 51071</p>\r\n+ <p>uniprot: Q9Y315</p>\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+ <p>ensembl: ENSG00000130313</p>\r\n+ <p>hgnc.symbol: PGLS</p>\r\n+ <p>ncbigene: 25796</p>\r\n+ <p>uniprot: O95336</p>\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+ <p>ensembl: ENSG00000157353</p>\r\n+ <p>hgnc.symbol: FCSK</p>\r\n+ <p>ncbigene: 197258</p>\r\n+ <p>uniprot: Q8N0W3</p>\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+ <p>ensembl: ENSG00000114268</p>\r\n+ <p>hgnc.symbol: PFKFB4</p>\r\n+ <p>ncbigene: 5210</p>\r\n+ <p>uniprot: Q16877</p>\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+ <p>ensembl: ENSG00000197417</p>\r\n+ <p>hgnc.symbol: SHPK</p>\r\n+ <p>ncbigene: 23729</p>\r\n+ <p>uniprot: Q9UHJ6</p>\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+ <p>Confidence Level: 0</p>\r\n+ <p>AUTHORS: PMID:5114731;PMID:5655259;PMID:6054986</p>\r\n+ <p>ec-code: 4.1.2.13</p>\r\n+ <p>metanetx.reaction: MNXR99460</p>\r\n+ <p>kegg.reaction: R02568</p>\r\n+ <p>bigg.reaction: FBA2</p>\r\n+ <p>SUBSYSTEM: Fructose and mannose metabolism</p>\r\n+ <p>EC_NUMBER: 4.1.2.13</p>\r\n+ <p>pmids: 5114731,5655259,6054986</p>\r\n+ <p>GENE_ASSOCIATION: ( ENSG00000109107 ) OR ( ENSG00000136872 ) OR ( ENSG00000149925 ) OR ( ENSG00000285043 )</p>\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' |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SBMLwizard/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SBMLwizard/test-data/XF_network.sbml Tue Jul 04 10:21:26 2023 +0000 |
| b |
| 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+ <p>GENE_ASSOCIATION: XFCFBP8418_018650</p>\n+ <p>SUBSYSTEM: Transport__Inner_Membrane</p>\n+ <p>EC_NUMBER: No_Assignment</p>\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+ <p>GENE_ASSOCIATION: XFCFBP8418_025070</p>\n+ <p>SUBSYSTEM: Cell_Envelope_Biosynthesis</p>\n+ <p>EC_NUMBER: 3.1.2.20</p>\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' |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SBMLwizard/test-data/XF_network_C_Side.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SBMLwizard/test-data/XF_network_C_Side.tab Tue Jul 04 10:21:26 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +M_atp_c +M_h2o_c +M_pi_c +M_adp_c +M_ppi_c +M_h_c |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SBMLwizard/test-data/XF_network_R_Seed.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SBMLwizard/test-data/XF_network_R_Seed.tab Tue Jul 04 10:21:26 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +R_ACGS +R_GLUN |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/Sbml2Graph/Sbml2Graph.xml --- a/build/tools/Sbml2Graph/Sbml2Graph.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/Sbml2Graph/Sbml2Graph.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.3.0"> +<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.4.0"> <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:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" $bipartite |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/Sbml2Tab/Sbml2Tab.xml --- a/build/tools/Sbml2Tab/Sbml2Tab.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/Sbml2Tab/Sbml2Tab.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="1.3.0"> +<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="1.4.0"> <description>Create a tabulated file from a SBML file</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): -i "$i" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlCheckBalance/SbmlCheckBalance.xml --- a/build/tools/SbmlCheckBalance/SbmlCheckBalance.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlCheckBalance/SbmlCheckBalance.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="1.3.0"> +<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="1.4.0"> <description>Check balance of all the reactions in a SBML.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.SbmlCheckBalance -sbml "$sbml" -out "$out" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml --- a/build/tools/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.3.0"> +<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.4.0"> <description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan': -cc "$colcharge" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml --- a/build/tools/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="1.3.0"> +<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="1.4.0"> <description>Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetEcsFromFile#if str($colec) != 'nan': -cec "$colec" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml --- a/build/tools/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="1.3.0"> +<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="1.4.0"> <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan': -cf "$colformula" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml --- a/build/tools/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="1.3.0"> +<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="1.4.0"> <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan': -cgpr "$colgpr" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml --- a/build/tools/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetIdsFromFile" name="SbmlSetIdsFromFile" version="1.3.0"> +<tool id="met4j_SbmlSetIdsFromFile" name="SbmlSetIdsFromFile" version="1.4.0"> <description>Set new ids to network objects from a tabulated file containing the old ids and the new ids</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetIdsFromFile#if str($colname) != 'nan': -cnew "$colname" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml --- a/build/tools/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="1.3.0"> +<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="1.4.0"> <description>Set names to network objects from a tabulated file containing the object ids and the names</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetNamesFromFile#if str($colname) != 'nan': -cname "$colname" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml --- a/build/tools/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.3.0"> +<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.4.0"> <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan': -cp "$colp" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml --- a/build/tools/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.3.0"> +<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.4.0"> <description>Add refs to network objects from a tabulated file containing the metabolite ids and the formulas</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan': -cr "$colRef" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml --- a/build/tools/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="1.3.0"> +<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="1.4.0"> <description>Create a tabulated file with metabolite attributes from a SBML file</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlToMetaboliteTable -s "$sbml" -o "$outputFile" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/ScopeNetwork/ScopeNetwork.xml --- a/build/tools/ScopeNetwork/ScopeNetwork.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/ScopeNetwork/ScopeNetwork.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.3.0"> +<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.4.0"> <description>Perform a network expansion from a set of compound seeds to create a scope network</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath" -s "$seedsFilePath" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SeedsAndTargets/SeedsAndTargets.xml --- a/build/tools/SeedsAndTargets/SeedsAndTargets.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SeedsAndTargets/SeedsAndTargets.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="1.3.0"> +<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="1.4.0"> <description>Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath" #if str($inputSide) != 'None': |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/SideCompoundsScan/SideCompoundsScan.xml --- a/build/tools/SideCompoundsScan/SideCompoundsScan.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/SideCompoundsScan/SideCompoundsScan.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="1.3.0"> +<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="1.4.0"> <description>Scan a network to identify side-compounds.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath" $sideOnly |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 build/tools/Tab2Sbml/Tab2Sbml.xml --- a/build/tools/Tab2Sbml/Tab2Sbml.xml Wed May 17 13:26:37 2023 +0000 +++ b/build/tools/Tab2Sbml/Tab2Sbml.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.3.0"> +<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.4.0"> <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan': -ci "$colid" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 data/XF_network_C_Seed.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/XF_network_C_Seed.tab Tue Jul 04 10:21:26 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +M_glu_D_c +M_xu5p_L_c +M_pep_c |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tests.html --- a/tests.html Wed May 17 13:26:37 2023 +0000 +++ b/tests.html Tue Jul 04 10:21:26 2023 +0000 |
| b |
| b"@@ -285,7 +285,7 @@\n var md = window.markdownit({\n html: true,\n });\n- target.innerHTML = 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</script>\n </body>\n </html>\n\\ No newline at end of file\n" |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/convert/SBMLwizard/SBMLwizard.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/SBMLwizard/SBMLwizard.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -0,0 +1,79 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="met4j_SBMLwizard" name="SBMLwizard" version="MET4J_VERSION_TEST"> + <description>General SBML model processing</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SBMLwizard -s "$inputPath" +#if str($inputSide) != 'None': + -rc "$inputSide" +#end if + $removeIsolated +#if str($inputReactions) != 'None': + -rr "$inputReactions" +#end if + $removeNoFlux +#if str($mergingStrat): + -mc "$mergingStrat" +#end if + $removeDuplicated +#if str($exchangeCompToRemove): + -rEX "$exchangeCompToRemove" +#end if + -o "$outputPath" +]]></command> + <inputs> + <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-rc" format="txt" label="file containing identifiers of compounds to remove from the metabolic network" name="inputSide" optional="true" type="data" value=""/> + <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/> + <param argument="-rr" format="txt" label="file containing identifiers of reactions to remove from the metabolic network" name="inputReactions" optional="true" type="data" value=""/> + <param argument="-r0" checked="false" falsevalue="" label="remove reactions with lower and upper flux bounds both set to 0.0" name="removeNoFlux" truevalue="-r0" type="boolean" value="false"/> + <param argument="-mc" label="merge compartments using the provided strategy. No merge by default. "by_name" can be used if names are consistent and unambiguous across compartments, "by_id" can be used if compartment suffix is present in compounds identifiers (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no"> + <option selected="true" value="no">no</option> + <option value="by_name">by_name</option> + <option value="by_id">by_id</option> + </param> + <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/> + <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="outputPath"/> + </outputs> + <tests> + <test> + <param name="inputPath" value="Human-GEM_pathways.xml"/> + <param name="removeIsolated" value="true"/> + <param name="removeNoFlux" value="true"/> + <param name="mergingStrat" value="by_id"/> + <param name="removeDuplicated" value="true"/> + <param name="exchangeCompToRemove" value="s"/> + <output ftype="sbml" name="outputPath"> + <assert_contents> + <has_text text="</sbml>"/> + </assert_contents> + </output> + </test> + <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="removeIsolated" value="true"/> + <param name="removeNoFlux" value="true"/> + <param name="removeDuplicated" value="true"/> + <param name="inputSide" value="XF_network_C_Side.tab"/> + <param name="inputReactions" value="XF_network_R_Seed.tab"/> + <output ftype="sbml" name="outputPath"> + <assert_contents> + <has_text text="</sbml>"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help> + <citations/> +</tool> |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/convert/SBMLwizard/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/SBMLwizard/test-data/Human-GEM_pathways.xml Tue Jul 04 10:21:26 2023 +0000 |
| b |
| 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+ <p>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.</p>\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+ <p>ensembl: ENSG00000023697</p>\r\n+ <p>hgnc.symbol: DERA</p>\r\n+ <p>ncbigene: 51071</p>\r\n+ <p>uniprot: Q9Y315</p>\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+ <p>ensembl: ENSG00000130313</p>\r\n+ <p>hgnc.symbol: PGLS</p>\r\n+ <p>ncbigene: 25796</p>\r\n+ <p>uniprot: O95336</p>\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+ <p>ensembl: ENSG00000157353</p>\r\n+ <p>hgnc.symbol: FCSK</p>\r\n+ <p>ncbigene: 197258</p>\r\n+ <p>uniprot: Q8N0W3</p>\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+ <p>ensembl: ENSG00000114268</p>\r\n+ <p>hgnc.symbol: PFKFB4</p>\r\n+ <p>ncbigene: 5210</p>\r\n+ <p>uniprot: Q16877</p>\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+ <p>ensembl: ENSG00000197417</p>\r\n+ <p>hgnc.symbol: SHPK</p>\r\n+ <p>ncbigene: 23729</p>\r\n+ <p>uniprot: Q9UHJ6</p>\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+ <p>Confidence Level: 0</p>\r\n+ <p>AUTHORS: PMID:5114731;PMID:5655259;PMID:6054986</p>\r\n+ <p>ec-code: 4.1.2.13</p>\r\n+ <p>metanetx.reaction: MNXR99460</p>\r\n+ <p>kegg.reaction: R02568</p>\r\n+ <p>bigg.reaction: FBA2</p>\r\n+ <p>SUBSYSTEM: Fructose and mannose metabolism</p>\r\n+ <p>EC_NUMBER: 4.1.2.13</p>\r\n+ <p>pmids: 5114731,5655259,6054986</p>\r\n+ <p>GENE_ASSOCIATION: ( ENSG00000109107 ) OR ( ENSG00000136872 ) OR ( ENSG00000149925 ) OR ( ENSG00000285043 )</p>\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' |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/convert/SBMLwizard/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/SBMLwizard/test-data/XF_network.sbml Tue Jul 04 10:21:26 2023 +0000 |
| b |
| 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+ <p>GENE_ASSOCIATION: XFCFBP8418_018650</p>\n+ <p>SUBSYSTEM: Transport__Inner_Membrane</p>\n+ <p>EC_NUMBER: No_Assignment</p>\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+ <p>GENE_ASSOCIATION: XFCFBP8418_025070</p>\n+ <p>SUBSYSTEM: Cell_Envelope_Biosynthesis</p>\n+ <p>EC_NUMBER: 3.1.2.20</p>\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' |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/convert/SBMLwizard/test-data/XF_network_C_Side.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/SBMLwizard/test-data/XF_network_C_Side.tab Tue Jul 04 10:21:26 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +M_atp_c +M_h2o_c +M_pi_c +M_adp_c +M_ppi_c +M_h_c |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/convert/SBMLwizard/test-data/XF_network_R_Seed.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/SBMLwizard/test-data/XF_network_R_Seed.tab Tue Jul 04 10:21:26 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +R_ACGS +R_GLUN |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/met4j.yml --- a/tools/met4j.yml Wed May 17 13:26:37 2023 +0000 +++ b/tools/met4j.yml Tue Jul 04 10:21:26 2023 +0000 |
| b |
| @@ -54,6 +54,9 @@ - name: Kegg2Sbml owner: metexplore tool_panel_section_id: met4j_convert + - name: SBMLwizard + owner: metexplore + tool_panel_section_id: met4j_convert - name: Sbml2Graph owner: metexplore tool_panel_section_id: met4j_convert |
| b |
| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/networkAnalysis/ChokePoint/ChokePoint.xml --- a/tools/networkAnalysis/ChokePoint/ChokePoint.xml Wed May 17 13:26:37 2023 +0000 +++ b/tools/networkAnalysis/ChokePoint/ChokePoint.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -8,14 +8,10 @@ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath" -#if str($sideCompoundFile) != 'None': - -s "$sideCompoundFile" -#end if -o "$outputPath" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/> </inputs> <outputs> <data format="tsv" name="outputPath"/> @@ -25,28 +21,16 @@ <param name="inputPath" value="XF_network.sbml"/> <output ftype="tsv" name="outputPath"> <assert_contents> - <has_n_lines n="202"/> + <has_n_lines n="695"/> <has_n_columns n="3"/> <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e <==> M_ade_p" n="1"/> - <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --> M_ru5p_L_c" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="XF_network.sbml"/> - <param name="sideCompoundFile" value="sides.txt"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="200"/> - <has_n_columns n="3"/> - <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e <==> M_ade_p" n="1" negate="true"/> - <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --> M_ru5p_L_c" n="1" negate="true"/> + <has_line_matching expression="R_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --> M_ac_c \+ M_gam6p_c" n="1"/> </assert_contents> </output> </test> </tests> <help><![CDATA[Compute the Choke points of a metabolic network. -Load points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target +Choke points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target See : Syed Asad Rahman, Dietmar Schomburg; Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinformatics 2006; 22 (14): 1767-1774. doi: 10.1093/bioinformatics/btl181]]></help> <citations/> </tool> |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/networkAnalysis/ChokePoint/test-data/sides.txt --- a/tools/networkAnalysis/ChokePoint/test-data/sides.txt Wed May 17 13:26:37 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -M_xu5p_L_c -M_ru5p_L_c -M_ade_e -M_ade_p \ No newline at end of file |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/networkAnalysis/MetaboRank/MetaboRank.xml --- a/tools/networkAnalysis/MetaboRank/MetaboRank.xml Wed May 17 13:26:37 2023 +0000 +++ b/tools/networkAnalysis/MetaboRank/MetaboRank.xml Tue Jul 04 10:21:26 2023 +0000 |
| [ |
| @@ -42,7 +42,19 @@ <outputs> <data format="tsv" name="output"/> </outputs> - <tests/> + <tests> + <test> + <param name="sbmlFilePath" value="XF_network.sbml"/> + <param name="seedsFilePath" value="XF_network_C_Seed.tab"/> + <param name="inputSide" value="XF_network_C_Side.tab"/> + <output name="output"> + <assert_contents> + <has_n_lines n="1100"/> + <has_n_columns n="11"/> + </assert_contents> + </output> + </test> + </tests> <help><O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/networkAnalysis/MetaboRank/test-data/weights.txt --- a/tools/networkAnalysis/MetaboRank/test-data/weights.txt Wed May 17 13:26:37 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -B 10 -C 1 \ No newline at end of file |
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| diff -r 7a6f2380fc1d -r 1436e9cde9c9 tools/tool_conf.xml --- a/tools/tool_conf.xml Wed May 17 13:26:37 2023 +0000 +++ b/tools/tool_conf.xml Tue Jul 04 10:21:26 2023 +0000 |
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| @@ -21,6 +21,7 @@ <section id="met4j_convert" name="Met4J - convert"/> <tool file="met4j/convert/FbcToNotes/FbcToNotes.xml"/> <tool file="met4j/convert/Kegg2Sbml/Kegg2Sbml.xml"/> + <tool file="met4j/convert/SBMLwizard/SBMLwizard.xml"/> <tool file="met4j/convert/Sbml2Graph/Sbml2Graph.xml"/> <tool file="met4j/convert/Sbml2Tab/Sbml2Tab.xml"/> <tool file="met4j/convert/Tab2Sbml/Tab2Sbml.xml"/> |