| Previous changeset 8:1274e2a62479 (2023-07-26) Next changeset 10:6a112eaf8f38 (2025-02-03) |
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Commit message:
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273 |
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modified:
Dockerfile build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml build/tools/ChokePoint/ChokePoint.xml build/tools/DegreeWeighting/DegreeWeighting.xml build/tools/DistanceMatrix/DistanceMatrix.xml build/tools/ExtractPathways/ExtractPathways.xml build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml build/tools/ExtractSubNetwork/ExtractSubNetwork.xml build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml build/tools/ExtractSubReactionNetwork/test-data/sides.txt build/tools/FbcToNotes/FbcToNotes.xml build/tools/GetGenesFromReactions/GetGenesFromReactions.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/ORApathwayEnrichment/ORApathwayEnrichment.xml build/tools/PrecursorNetwork/PrecursorNetwork.xml build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml build/tools/Sbml2Graph/Sbml2Graph.xml build/tools/Sbml2Tab/Sbml2Tab.xml build/tools/SbmlCheckBalance/SbmlCheckBalance.xml build/tools/ScopeNetwork/ScopeNetwork.xml build/tools/SeedsAndTargets/SeedsAndTargets.xml build/tools/SideCompoundsScan/SideCompoundsScan.xml build/tools/Tab2Sbml/Tab2Sbml.xml build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml tests.html tools/attributes/ExtractPathways/ExtractPathways.xml tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml tools/convert/FbcToNotes/FbcToNotes.xml tools/convert/Kegg2Sbml/Kegg2Sbml.xml tools/convert/Sbml2Graph/Sbml2Graph.xml tools/convert/Sbml2Tab/Sbml2Tab.xml tools/convert/Tab2Sbml/Tab2Sbml.xml tools/mapping/NameMatcher/NameMatcher.xml tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml tools/met4j.yml tools/networkAnalysis/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml tools/networkAnalysis/ChokePoint/ChokePoint.xml tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml tools/networkAnalysis/ExtractSubReactionNetwork/test-data/sides.txt tools/networkAnalysis/LoadPoint/LoadPoint.xml tools/networkAnalysis/MetaboRank/MetaboRank.xml tools/networkAnalysis/NetworkSummary/NetworkSummary.xml tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml tools/networkAnalysis/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml tools/tool_conf.xml |
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added:
build/tools/CreateMetaNetwork/CreateMetaNetwork.xml build/tools/CreateMetaNetwork/test-data/ECOL.xml build/tools/CreateMetaNetwork/test-data/Human-GEM_pathways.xml build/tools/ExtractAnnotations/ExtractAnnotations.xml build/tools/ExtractAnnotations/test-data/Human-GEM_pathways.xml build/tools/GetBiggModelProteome/GetBiggModelProteome.xml build/tools/GetEntities/GetEntities.xml build/tools/GetEntities/test-data/Human-GEM_pathways.xml build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.xml build/tools/GetMetaboliteAttributes/test-data/tests.tsv build/tools/GetMetaboliteAttributes/test-data/toy_model.xml build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml build/tools/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab build/tools/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab build/tools/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways.xml build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml build/tools/Sbml2CompoundGraph/test-data/XF_network.sbml build/tools/Sbml2CompoundGraph/test-data/XF_network_C_Side.tab build/tools/Sbml2PathwayNet/Sbml2PathwayNet.xml 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 build/tools/SetCharges/SetCharges.xml build/tools/SetCharges/test-data/XF_network.sbml build/tools/SetCharges/test-data/charges.tsv build/tools/SetCharges/test-data/chargesDifferentColumns.tsv build/tools/SetCharges/test-data/chargesWithComment.tsv build/tools/SetCharges/test-data/chargesXF.tsv build/tools/SetCharges/test-data/toy_model.xml build/tools/SetChemicalFormulas/SetChemicalFormulas.xml build/tools/SetChemicalFormulas/test-data/formula.tsv build/tools/SetChemicalFormulas/test-data/formulaBad.tsv build/tools/SetChemicalFormulas/test-data/toy_model.xml build/tools/SetEcNumbers/SetEcNumbers.xml build/tools/SetEcNumbers/test-data/ec.tsv build/tools/SetEcNumbers/test-data/ecBad.tsv build/tools/SetEcNumbers/test-data/toy_model.xml build/tools/SetGprs/SetGprs.xml build/tools/SetGprs/test-data/gpr.tsv build/tools/SetGprs/test-data/gprBad.tsv build/tools/SetGprs/test-data/toy_model.xml build/tools/SetIds/SetIds.xml build/tools/SetIds/test-data/XF_network.sbml build/tools/SetIds/test-data/idCompartments.tsv build/tools/SetIds/test-data/idGenes.tsv build/tools/SetIds/test-data/idMetabolites.tsv build/tools/SetIds/test-data/idPathways.tsv build/tools/SetIds/test-data/idReactions.tsv build/tools/SetIds/test-data/toy_model.xml build/tools/SetNames/SetNames.xml build/tools/SetNames/test-data/XF_network.sbml build/tools/SetNames/test-data/namesGenes.tsv build/tools/SetNames/test-data/namesMetabolites.tsv build/tools/SetNames/test-data/namesPathways.tsv build/tools/SetNames/test-data/namesReactions.tsv build/tools/SetNames/test-data/toy_model.xml build/tools/SetPathways/SetPathways.xml build/tools/SetPathways/test-data/pathways.tsv build/tools/SetPathways/test-data/pathwaysOtherSep.tsv build/tools/SetPathways/test-data/toy_model.xml build/tools/SetReferences/SetReferences.xml build/tools/SetReferences/test-data/refs.tsv build/tools/SetReferences/test-data/toy_model.xml met4j-galaxy.iml tools/attributes/ExtractAnnotations/ExtractAnnotations.xml tools/attributes/ExtractAnnotations/test-data/Human-GEM_pathways.xml tools/attributes/GetEntities/GetEntities.xml tools/attributes/GetEntities/test-data/Human-GEM_pathways.xml tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml tools/attributes/GetMetaboliteAttributes/test-data/tests.tsv tools/attributes/GetMetaboliteAttributes/test-data/toy_model.xml tools/attributes/SetCharges/SetCharges.xml tools/attributes/SetCharges/test-data/XF_network.sbml tools/attributes/SetCharges/test-data/charges.tsv tools/attributes/SetCharges/test-data/chargesDifferentColumns.tsv tools/attributes/SetCharges/test-data/chargesWithComment.tsv tools/attributes/SetCharges/test-data/chargesXF.tsv tools/attributes/SetCharges/test-data/toy_model.xml tools/attributes/SetChemicalFormulas/SetChemicalFormulas.xml tools/attributes/SetChemicalFormulas/test-data/formula.tsv tools/attributes/SetChemicalFormulas/test-data/formulaBad.tsv tools/attributes/SetChemicalFormulas/test-data/toy_model.xml tools/attributes/SetEcNumbers/SetEcNumbers.xml tools/attributes/SetEcNumbers/test-data/ec.tsv tools/attributes/SetEcNumbers/test-data/ecBad.tsv tools/attributes/SetEcNumbers/test-data/toy_model.xml tools/attributes/SetGprs/SetGprs.xml tools/attributes/SetGprs/test-data/gpr.tsv tools/attributes/SetGprs/test-data/gprBad.tsv tools/attributes/SetGprs/test-data/toy_model.xml tools/attributes/SetIds/SetIds.xml tools/attributes/SetIds/test-data/XF_network.sbml tools/attributes/SetIds/test-data/idCompartments.tsv tools/attributes/SetIds/test-data/idGenes.tsv tools/attributes/SetIds/test-data/idMetabolites.tsv tools/attributes/SetIds/test-data/idPathways.tsv tools/attributes/SetIds/test-data/idReactions.tsv tools/attributes/SetIds/test-data/toy_model.xml tools/attributes/SetNames/SetNames.xml tools/attributes/SetNames/test-data/XF_network.sbml tools/attributes/SetNames/test-data/namesGenes.tsv tools/attributes/SetNames/test-data/namesMetabolites.tsv tools/attributes/SetNames/test-data/namesPathways.tsv tools/attributes/SetNames/test-data/namesReactions.tsv tools/attributes/SetNames/test-data/toy_model.xml tools/attributes/SetPathways/SetPathways.xml tools/attributes/SetPathways/test-data/pathways.tsv tools/attributes/SetPathways/test-data/pathwaysOtherSep.tsv tools/attributes/SetPathways/test-data/toy_model.xml tools/attributes/SetReferences/SetReferences.xml tools/attributes/SetReferences/test-data/refs.tsv tools/attributes/SetReferences/test-data/toy_model.xml tools/bigg/GetBiggModelProteome/GetBiggModelProteome.xml tools/convert/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml tools/convert/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab tools/convert/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab tools/convert/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways.xml tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml tools/convert/Sbml2CompoundGraph/test-data/XF_network.sbml tools/convert/Sbml2CompoundGraph/test-data/XF_network_C_Side.tab tools/convert/Sbml2PathwayNet/Sbml2PathwayNet.xml 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/reconstruction/CreateMetaNetwork/CreateMetaNetwork.xml tools/reconstruction/CreateMetaNetwork/test-data/ECOL.xml tools/reconstruction/CreateMetaNetwork/test-data/Human-GEM_pathways.xml |
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removed:
build/tools/CarbonSkeletonNet/CarbonSkeletonNet.xml build/tools/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab build/tools/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab build/tools/CarbonSkeletonNet/test-data/Human-GEM_pathways.xml build/tools/CompoundNet/CompoundNet.xml build/tools/CompoundNet/test-data/XF_network.sbml build/tools/CompoundNet/test-data/XF_network_C_Side.tab build/tools/DecomposeSBML/DecomposeSBML.xml build/tools/DecomposeSBML/test-data/Human-GEM_pathways.xml build/tools/ExtractSbmlAnnot/ExtractSbmlAnnot.xml build/tools/ExtractSbmlAnnot/test-data/Human-GEM_pathways.xml build/tools/GetModelProteome/GetModelProteome.xml build/tools/GetModelProteome/proteome.fas build/tools/PathwayNet/PathwayNet.xml 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 build/tools/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml build/tools/SbmlSetChargesFromFile/test-data/XF_network.sbml build/tools/SbmlSetChargesFromFile/test-data/charges.tsv build/tools/SbmlSetChargesFromFile/test-data/chargesDifferentColumns.tsv build/tools/SbmlSetChargesFromFile/test-data/chargesWithComment.tsv build/tools/SbmlSetChargesFromFile/test-data/chargesXF.tsv build/tools/SbmlSetChargesFromFile/test-data/toy_model.xml build/tools/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml build/tools/SbmlSetEcsFromFile/test-data/ec.tsv build/tools/SbmlSetEcsFromFile/test-data/ecBad.tsv build/tools/SbmlSetEcsFromFile/test-data/toy_model.xml build/tools/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml build/tools/SbmlSetFormulasFromFile/test-data/formula.tsv build/tools/SbmlSetFormulasFromFile/test-data/formulaBad.tsv build/tools/SbmlSetFormulasFromFile/test-data/toy_model.xml build/tools/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml build/tools/SbmlSetGprsFromFile/test-data/gpr.tsv build/tools/SbmlSetGprsFromFile/test-data/gprBad.tsv build/tools/SbmlSetGprsFromFile/test-data/toy_model.xml build/tools/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml build/tools/SbmlSetIdsFromFile/test-data/XF_network.sbml build/tools/SbmlSetIdsFromFile/test-data/idCompartments.tsv build/tools/SbmlSetIdsFromFile/test-data/idGenes.tsv build/tools/SbmlSetIdsFromFile/test-data/idMetabolites.tsv build/tools/SbmlSetIdsFromFile/test-data/idPathways.tsv build/tools/SbmlSetIdsFromFile/test-data/idReactions.tsv build/tools/SbmlSetIdsFromFile/test-data/toy_model.xml build/tools/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml build/tools/SbmlSetNamesFromFile/test-data/XF_network.sbml build/tools/SbmlSetNamesFromFile/test-data/namesGenes.tsv build/tools/SbmlSetNamesFromFile/test-data/namesMetabolites.tsv build/tools/SbmlSetNamesFromFile/test-data/namesPathways.tsv build/tools/SbmlSetNamesFromFile/test-data/namesReactions.tsv build/tools/SbmlSetNamesFromFile/test-data/toy_model.xml build/tools/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml build/tools/SbmlSetPathwaysFromFile/test-data/pathways.tsv build/tools/SbmlSetPathwaysFromFile/test-data/pathwaysOtherSep.tsv build/tools/SbmlSetPathwaysFromFile/test-data/toy_model.xml build/tools/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml build/tools/SbmlSetRefsFromFile/test-data/refs.tsv build/tools/SbmlSetRefsFromFile/test-data/toy_model.xml build/tools/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml build/tools/SbmlToMetaboliteTable/test-data/tests.tsv build/tools/SbmlToMetaboliteTable/test-data/toy_model.xml tools/attributes/DecomposeSBML/DecomposeSBML.xml tools/attributes/DecomposeSBML/test-data/Human-GEM_pathways.xml tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml tools/attributes/ExtractSbmlAnnot/test-data/Human-GEM_pathways.xml tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml tools/attributes/SbmlSetChargesFromFile/test-data/XF_network.sbml tools/attributes/SbmlSetChargesFromFile/test-data/charges.tsv tools/attributes/SbmlSetChargesFromFile/test-data/chargesDifferentColumns.tsv tools/attributes/SbmlSetChargesFromFile/test-data/chargesWithComment.tsv tools/attributes/SbmlSetChargesFromFile/test-data/chargesXF.tsv tools/attributes/SbmlSetChargesFromFile/test-data/toy_model.xml tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml tools/attributes/SbmlSetEcsFromFile/test-data/ec.tsv tools/attributes/SbmlSetEcsFromFile/test-data/ecBad.tsv tools/attributes/SbmlSetEcsFromFile/test-data/toy_model.xml tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml tools/attributes/SbmlSetFormulasFromFile/test-data/formula.tsv tools/attributes/SbmlSetFormulasFromFile/test-data/formulaBad.tsv tools/attributes/SbmlSetFormulasFromFile/test-data/toy_model.xml tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml tools/attributes/SbmlSetGprsFromFile/test-data/gpr.tsv tools/attributes/SbmlSetGprsFromFile/test-data/gprBad.tsv tools/attributes/SbmlSetGprsFromFile/test-data/toy_model.xml tools/attributes/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml tools/attributes/SbmlSetIdsFromFile/test-data/XF_network.sbml tools/attributes/SbmlSetIdsFromFile/test-data/idCompartments.tsv tools/attributes/SbmlSetIdsFromFile/test-data/idGenes.tsv tools/attributes/SbmlSetIdsFromFile/test-data/idMetabolites.tsv tools/attributes/SbmlSetIdsFromFile/test-data/idPathways.tsv tools/attributes/SbmlSetIdsFromFile/test-data/idReactions.tsv tools/attributes/SbmlSetIdsFromFile/test-data/toy_model.xml tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml tools/attributes/SbmlSetNamesFromFile/test-data/XF_network.sbml tools/attributes/SbmlSetNamesFromFile/test-data/namesGenes.tsv tools/attributes/SbmlSetNamesFromFile/test-data/namesMetabolites.tsv tools/attributes/SbmlSetNamesFromFile/test-data/namesPathways.tsv tools/attributes/SbmlSetNamesFromFile/test-data/namesReactions.tsv tools/attributes/SbmlSetNamesFromFile/test-data/toy_model.xml tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml tools/attributes/SbmlSetPathwaysFromFile/test-data/pathways.tsv tools/attributes/SbmlSetPathwaysFromFile/test-data/pathwaysOtherSep.tsv tools/attributes/SbmlSetPathwaysFromFile/test-data/toy_model.xml tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml tools/attributes/SbmlSetRefsFromFile/test-data/refs.tsv tools/attributes/SbmlSetRefsFromFile/test-data/toy_model.xml tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml tools/attributes/SbmlToMetaboliteTable/test-data/tests.tsv tools/attributes/SbmlToMetaboliteTable/test-data/toy_model.xml tools/bigg/GetModelProteome/GetModelProteome.xml tools/bigg/GetModelProteome/proteome.fas 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/CarbonSkeletonNet/CarbonSkeletonNet.xml tools/networkAnalysis/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab tools/networkAnalysis/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab tools/networkAnalysis/CarbonSkeletonNet/test-data/Human-GEM_pathways.xml tools/networkAnalysis/CompoundNet/CompoundNet.xml tools/networkAnalysis/CompoundNet/test-data/XF_network.sbml tools/networkAnalysis/CompoundNet/test-data/XF_network_C_Side.tab tools/networkAnalysis/PathwayNet/PathwayNet.xml |
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| diff -r 1274e2a62479 -r 0976a6257300 Dockerfile --- a/Dockerfile Wed Jul 26 15:33:45 2023 +0000 +++ b/Dockerfile Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,75 +1,83 @@ -FROM python:3.10-buster +FROM python:3.9.12-slim-bullseye # set author -MAINTAINER Ludovic Cottret <ludovic.cottret@inrae.fr> +LABEL maintainer "Ludovic Cottret <ludovic.cottret@inrae.fr>" # set encoding ENV LC_ALL en_US.UTF-8 ENV LANG en_US.UTF-8 -ENV PLANEMO_VENV_LOCATION /planemo-venv -ENV CONDA /tmp/conda +ENV DEBIAN_FRONTEND=noninteractive + + +RUN useradd -ms /bin/bash galaxy_user +# RUN usermod -aG sudo galaxy_user -RUN \ - apt-get update \ - && apt-get install -y --no-install-recommends \ - ed \ - less \ - locales \ - vim-tiny \ - wget \ - ca-certificates \ - fonts-texgyre \ - build-essential \ - libseccomp-dev \ - pkg-config \ - squashfs-tools \ - cryptsetup \ - && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \ - && locale-gen en_US.utf8 \ - && /usr/sbin/update-locale LANG=en_US.UTF-8 \ - && echo "deb http://http.debian.net/debian buster main" > /etc/apt/sources.list.d/debian-unstable.list \ - && echo 'APT::Default-Release "buster";' > /etc/apt/apt.conf.d/default \ - && echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90local-no-recommends \ - && apt-get update \ - && apt-get upgrade -y \ - && apt-get install -y --no-install-recommends \ - git \ - littler \ - libhdf5-dev \ - python-virtualenv \ - && pip install virtualenv \ - && python -m virtualenv "$PLANEMO_VENV_LOCATION" \ - && . "$PLANEMO_VENV_LOCATION"/bin/activate \ - && pip install --upgrade pip setuptools \ - && pip install planemo numpy \ - && apt-get clean autoclean \ - && apt-get autoremove --yes \ - && rm -rf /var/lib/{apt,dpkg,cache,log}/ \ - && rm -rf /usr/bin/X11 \ - && rm -rf /tmp/* +# Install dependencies +RUN apt-get update \ + && apt-get install -y \ + curl \ + sudo \ + build-essential \ + libseccomp-dev \ + autoconf \ + automake \ + cryptsetup \ + fuse2fs \ + git \ + fuse \ + libfuse-dev \ + libglib2.0-dev \ + libseccomp-dev \ + libtool \ + pkg-config \ + runc \ + squashfs-tools \ + squashfs-tools-ng \ + uidmap \ + wget \ + zlib1g-dev + +# Install planemo +RUN pip install --upgrade pip \ + && pip install planemo SHELL ["/bin/bash", "-c"] +# Install GO RUN \ - export VERSION=1.17.2 OS=linux ARCH=amd64 \ - && wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz \ - && tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz \ - && rm go$VERSION.$OS-$ARCH.tar.gz \ - && echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \ + export VERSION=1.17.2 OS=linux ARCH=amd64 \ + && wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz \ + && tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz \ + && rm go$VERSION.$OS-$ARCH.tar.gz \ + && echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \ && source ~/.bashrc +# Install Singularity RUN \ echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \ && source ~/.bashrc \ - && export VERSION=3.10.0 \ - && wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz \ - && tar -xzf singularity-ce-${VERSION}.tar.gz \ + && export VERSION=3.10.0 \ + && wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz \ + && tar -xzf singularity-ce-${VERSION}.tar.gz \ && cd singularity-ce-${VERSION} \ - && ./mconfig && \ - make -C builddir && \ - make -C builddir install + && ./mconfig \ + && make -C builddir \ + && make -C builddir install \ + && cd .. \ + && rm -rf singularity-ce-${VERSION} singularity-ce-${VERSION}.tar.gz + +# Clean + +RUN apt-get clean autoclean \ + && apt-get autoremove --yes \ + && rm -rf /var/lib/{apt,dpkg,cache,log}/ \ + && rm -rf /usr/bin/X11 \ + && rm -rf /tmp/* + + +# USER galaxyuser CMD [] |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml --- a/build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="develop"> <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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.BipartiteDistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -42,7 +42,7 @@ </outputs> <tests/> <help><![CDATA[Create a compound to reactions distance matrix. -The distance between two nodes (metabolite or reaction) is computed as the length of the shortest path connecting the two in the bipartite graph, Bipartite graph are composed of two distinct sets of nodes and two nodes can be linked only if they are from distinct sets. +The distance between two nodes (metabolite or reaction) is computed as the length of the shortest path connecting the two in the bipartite graph, Bipartite graphs are composed of two distinct sets of nodes and two nodes can be linked only if they are from distinct sets. Therefore a metabolite node can be linked to a reaction node if the metabolite is a substrate or product of the reaction. An optional custom edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path.Custom weighting can be provided in a file. In that case, edges without weight are ignored during path search. If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/CarbonSkeletonNet/CarbonSkeletonNet.xml --- a/build/tools/CarbonSkeletonNet/CarbonSkeletonNet.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,122 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath" - -g "$inputAAM" - $keepSingleCarbon - $mergeComp - $mergeEdges - $removeIsolated - $undirected - $computeWeight - $asMatrix - $main - $fromIndexes - -o "$outputPath" -]]></command> - <inputs> - <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-g" format="gsam" label="input GSAM file" name="inputAAM" optional="false" type="data" value=""/> - <param argument="-ks" checked="false" falsevalue="" label="keep edges involving single-carbon compounds, such as CO2 (requires formulas in SBML)" name="keepSingleCarbon" truevalue="-ks" type="boolean" value="false"/> - <param argument="-mc" checked="false" falsevalue="" label="merge compartments (requires unique compound names that are consistent across compartments)" name="mergeComp" truevalue="-mc" type="boolean" value="false"/> - <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/> - <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> - <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/> - <param argument="-tp" checked="false" falsevalue="" label="set transition probability as weight" name="computeWeight" truevalue="-tp" type="boolean" value="false"/> - <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/> - <param argument="-main" checked="false" falsevalue="" label="Compute RPAIRS-like tags and keep only main transitions for each reaction" name="main" truevalue="-main" type="boolean" value="false"/> - <param argument="-i" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-i" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="gml" name="outputPath"/> - </outputs> - <tests> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2602"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="keepSingleCarbon" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2629"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="mergeComp" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2406"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="mergeEdges" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2071"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="removeIsolated" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2490"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="undirected" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="3214"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="asMatrix" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="112"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/> - <param name="fromIndexes" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2611"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produce a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) perform atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab --- a/build/tools/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab --- a/build/tools/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,206 +0,0 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. 23-21-19-17-16\tM_m01761c\t230.019153942\t23-21-19-17-16 . 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t260.029718626\t46-44-42-41-38-37\tM_m02955c\t339.99604914799994\t44-46-37-38-42-41\tR_HMR_4775\t79.96633052199996\t44,46,37,38,41,42\n-M_m02453c\t180.06338810399998\t42-40-38-36-34-33\tM_m02455c\t260.029718626\t33-34-42-40-38-36\tR_HMR_4490\t79.96633052199999\t33,34,36,38,40,42\n-M_m01961c\t258.01406856200003\t15-13-11-5-4-2\tM_m01169c\t276.024633246\t5-4-11-13-15-2\tR_HMR_4625\t18.010564683999974\t11,13,2,4,15,5\n-M_m01745c\t180.06338810399998\t42-40-38-37-34-33\tM_tag1p_D_c\t260.029718626\t37-38-40-42-34-33\tR_KHK3\t79.96633052199999\t33,34,37,38,40,42\n-M_m01746c\t260.029718626\t15-13-11-10-7-6\tM_m01690c\t169.99802457399997\t15-7-6\tR_HMR_8762\t90.031694052\t15,6,7\n-M_m01285c\t427.02941494\t30-28-26-24-22-21-19-17-15-14\tM_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tR_HMR_9800\t79.96633052199996\t22,24,14,26,15,28,17,19,30,21\n-M_m01159c\t164.06847348399998\t41-39-37-36-35-33\tM_m02372c\t244.034804006\t33-41-39-37-35-36\tR_HMR_4402\t79.96633052200002\t33,35,36,37,39,41\n-M_m01939c\t169.998024574\t8-6-4\tM_m00640c\t214.024239322\t8-6-4-3-2\tR_HMR_4398\t44.026214748\t4,6,8\n-M_m02845c\t230.01915394199997\t40-38-36-34-33\tM_m02806c\t389.951814986\t33-40-38-36-34\tR_HMR_4052\t159.932661044\t33,34,36,38,40\n-M_m01840c\t180.06338810399998\t55-53-46-47-49-51\tM_m01682c\t182.07903816799998\t55-53-51-49-47-46\tR_HMR_4315\t2.015650063999999\t55,46,47,49,51,53\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/CarbonSkeletonNet/test-data/Human-GEM_pathways.xml --- a/build/tools/CarbonSkeletonNet/test-data/Human-GEM_pathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,7661 +0,0 @@\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 1274e2a62479 -r 0976a6257300 build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml --- a/build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="develop"> <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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type): -f "$type" @@ -65,6 +65,10 @@ <data format="tsv" name="outputPath"/> </outputs> <tests/> - <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search. See McSha et al. 2003 (https://doi.org/10.1093/bioinformatics/btg217), Rahman et al. 2005 (https://doi.org/10.1093/bioinformatics/bti116) and Pertusi et al. 2014 (https://doi.org/10.1093/bioinformatics/btu760)]]></help> - <citations/> + <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search.]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btg217</citation> + <citation type="doi">10.1093/bioinformatics/bti116</citation> + <citation type="doi">10.1093/bioinformatics/btu760</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ChokePoint/ChokePoint.xml --- a/build/tools/ChokePoint/ChokePoint.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ChokePoint/ChokePoint.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ChokePoint" name="ChokePoint" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ChokePoint" name="ChokePoint" version="develop"> <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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath" -o "$outputPath" @@ -18,19 +18,130 @@ </outputs> <tests> <test> - <param name="inputPath" value="XF_network.sbml"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <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_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --> M_ac_c \+ M_gam6p_c" n="1"/> - </assert_contents> - </output> - </test> + + + + + + + + + + + + <param name="inputPath" value="XF_network.sbml"/> + + + + + + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <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_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. -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/> +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.]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btl181</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/CompoundNet/CompoundNet.xml --- a/build/tools/CompoundNet/CompoundNet.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,78 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_CompoundNet" name="CompoundNet" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath" -#if str($inputSide) != 'None': - -sc "$inputSide" -#end if -#if str($mergingStrat): - -mc "$mergingStrat" -#end if - $mergeEdges - $removeIsolated - $degree -#if str($weightFile) != 'None': - -cw "$weightFile" -#end if - $undirected - $computeWeight - $asMatrix - -o "$outputPath" -]]></command> - <inputs> - <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/> - <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (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="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/> - <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> - <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/> - <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> - <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/> - <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/> - <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="gml" name="outputPath"/> - </outputs> - <tests> - <test> - <param name="inputPath" value="XF_network.sbml"/> - <param name="inputSide" value="XF_network_C_Side.tab"/> - <output name="outputPath"> - <assert_contents> - <has_line_matching expression=".*node.*" n="1101"/> - <has_line_matching expression=".*edge.*" n="5581"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="XF_network.sbml"/> - <param name="inputSide" value="XF_network_C_Side.tab"/> - <param name="undirected" value="true"/> - <param name="computeWeight" value="true"/> - <param name="removeIsolated" value="true"/> - <param name="degree" value="true"/> - <param name="mergingStrat" value="by_id"/> - <output name="outputPath"> - <assert_contents> - <has_line_matching expression=".*node.*" n="793"/> - <has_line_matching expression=".*edge.*" n="9372"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. -While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations. -In contrary to the SBML2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree² weighting to get relevant structure without structural data.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/CompoundNet/test-data/XF_network.sbml --- a/build/tools/CompoundNet/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 build/tools/CompoundNet/test-data/XF_network_C_Side.tab --- a/build/tools/CompoundNet/test-data/XF_network_C_Side.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -M_atp_c -M_h2o_c -M_pi_c -M_adp_c -M_ppi_c -M_h_c |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/CreateMetaNetwork/CreateMetaNetwork.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/CreateMetaNetwork/CreateMetaNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,210 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="develop"> + <description>Create a Meta-Network from two sub-networks in SBML format.</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath" + -n2 "$sbml2FilePath" + -n1ex "$external1" + -n2ex "$external2" +#if str($n1prefix): + -n1px "$n1prefix" +#end if +#if str($n2prefix): + -n2px "$n2prefix" +#end if + $keepCompartment + $firstIsMeta +#if str($mergingCriterion): + -mc "$mergingCriterion" +#end if + -o "$outputPath" +]]></command> + <inputs> + <param argument="-n1" format="sbml" label="input SBML file: path to first network, in sbml format." name="sbml1FilePath" optional="false" type="data" value=""/> + <param argument="-n2" format="" label="input SBML file: path to second network, in sbml format." name="sbml2FilePath" optional="false" type="data" value=""/> + <param argument="-n1ex" label="external compartment identifier in first network." name="external1" optional="false" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-n2ex" label="external compartment identifier in second network." name="external2" optional="false" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-n1px" label="prefix that will be added to first network's entities identifiers" name="n1prefix" optional="true" type="text" value="Net1_"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-n2px" label="prefix that will be added to second network's entities identifiers" name="n2prefix" optional="true" type="text" value="Net2_"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-k" checked="false" falsevalue="" label="keep the original external compartments in the meta-network, otherwise, they will be fused into the new shared external compartment" name="keepCompartment" truevalue="-k" type="boolean" value="false"/> + <param argument="-n1meta" checked="false" falsevalue="" label="treat first network as meta-network, allowing more than two sub-models with iterative fusions. This will overwrite shared compartment and pool compounds (which must follow the "pool_" prefix convention) and will ignore --n1prefix argument" name="firstIsMeta" truevalue="-n1meta" type="boolean" value="false"/> + <param argument="-mc" label="field used to identify the same metabolites across the two different networks. "by_name"/"by_id" can be used if names/identifiers are consistent and unambiguous across source models, "by_metanetx" can be used if models contains MetaNetX identifiers in annotation field using standard miriam format." name="mergingCriterion" optional="true" type="select" value="by_name"> + <option value="by_metanetx">by_metanetx</option> + <option selected="true" value="by_name">by_name</option> + <option value="by_id">by_id</option> + </param> + </inputs> + <outputs> + <data format="sbml" name="outputPath"/> + </outputs> + <tests> + <test> + + + + + + + + + + + <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/> + + + + + + + + + + + <param name="sbml2FilePath" value="ECOL.xml"/> + + + + + + + + + + + <param name="external1" value="s"/> + + + + + + + + + + + <param name="external2" value="e"/> + + + + + + + + + + + <param name="n1prefix" value="hsa"/> + + + + + + + + + + + <param name="n2prefix" value="eco"/> + + + + + + + + + + + <param name="mergingCriterion" value="by_metanetx"/> + + + + + + + + + + + <output ftype="sbml" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <has_text text="</sbml>"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> + </tests> + <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format. +A meta-network is a single model which contains several sub-networks that remains individualized within the meta-network (as opposed to model fusion), but which can share some of their components with other sub-networks through a shared "medium" compartment.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/CreateMetaNetwork/test-data/ECOL.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/CreateMetaNetwork/test-data/ECOL.xml Fri Jan 31 18:28:53 2025 +0000 |
| b |
| b'@@ -0,0 +1,138833 @@\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="iML1515" metaid="iML1515" name="Escherichia coli str. K-12 substr. MG1655">\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="#iML1515">\r\n+ <bqbiol:hasProperty>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/pubmed/29020004"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/taxonomy/511145"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:hasProperty>\r\n+ <bqbiol:is>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/bigg.model/iML1515"/>\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_Ec_iML1515_core_75p37M"/>\r\n+ </fbc:listOfFluxObjectives>\r\n+ </fbc:objective>\r\n+ </fbc:listOfObjectives>\r\n+ <fbc:listOfGeneProducts>\r\n+ <fbc:geneProduct fbc:id="b4054" fbc:label="b4054" fbc:name="b4054" metaid="_19a85f06-f4d2-4ca4-962d-280d860d0188"/>\r\n+ <fbc:geneProduct fbc:id="b4053" fbc:label="b4053" fbc:name="b4053" metaid="_3320c40d-844a-45b2-a996-49c250766d53"/>\r\n+ <fbc:geneProduct fbc:id="b4298" fbc:label="b4298" fbc:name="b4298" metaid="_428fe2b1-ed44-4ef1-a55e-e9a88f70e43c"/>\r\n+ <fbc:geneProduct fbc:id="b4055" fbc:label="b4055" fbc:name="b4055" metaid="d3169d49-b4b4-439a-ba53-bb6292583779"/>\r\n+ <fbc:geneProduct fbc:id="b4297" fbc:label="b4297" fbc:name="b4297" metaid="_388e6eb0-5734-4c6e-9ef3-b927d0ee6f80"/>\r\n+ <fbc:geneProduct fbc:id="b4291" fbc:label="b4291" fbc:name="b4291" metaid="_9dd0f62e-2f14-4bef-b52a-262c735f727e"/>\r\n+ <fbc:geneProduct fbc:id="b0929" fbc:label="b0929" fbc:name="b0929" metaid="_337058ef-dd29-4e6e-861b-0c9a3c8ca11e"/>\r\n+ <fbc:geneProduct fbc:id="b0928" fbc:label="b0928" fbc:name="b0928" metaid="_2442f6a8-23e0-4e7d-99d6-3231f1260af1"/>\r\n+ <fbc:geneProduct fbc:id="b4290" fbc:label="b4290" fbc:name="b4290" metaid="cb5b0ae1-c107-4e9d-87bb-ca77a4e3d321"/>\r\n+ <fbc:geneProduct fbc:id="b0925" fbc:label="b0925" fbc:name="b0925" metaid="_80d0d7b3-f687-4841-8710-c3fe1788eb09"/>\r\n+ <fbc:geneProduct fbc:id="b4289" fbc:label="b4289" fbc:name="b4289" metaid="_813528ea-ec16-47fe-87cb-9dec6c6b78e2"/>\r\n+ <fbc:geneProduct fbc:id="b3199" fbc:label="b3199" fbc:name="b3199" metaid="_691a4ce9-01cd-4521-9e44-ae134a3d2a7f"/>\r\n+ <fbc:geneProduct fbc:id="b4288" fbc:label="b4288" fbc:name="b4288" metaid="fe7c001f-5b97-4a68-b421-36b27339b0dd"/>\r\n+ <fbc:geneProduct fbc:id="b4042" fbc:label="b4042" fbc:name="b4042" metaid="a9592745-8729-473a-9cb6-d5827d734dda"/>\r\n+ <fbc:geneProduct fbc:id="b3196" fbc:label="b3196" fbc:name="b3196" metaid="fd61ed6b-3ce6-42c8-ac48-d8ea58fc2bac"/>\r\n+ <fbc:geneProduct fbc:id="b3197" fbc:label="b3197" fbc:name="b3197" metaid="c9c8d396-7abc-4f97-8994-3a3e334ed6b1"/>\r\n+ <fbc:geneProduct fbc:id="b4287" fbc:label="b4287" fbc:name="b4287" metaid="c7589f3b-726a-4909-9514-d9eb40ef6815"/>\r\n+ <fbc:geneProduct fbc:id="b3198" fbc:label="b3198" fbc:name="b3198" metaid="bc09d6b2-a4bc-463c-bec4-8cfa2dd246cd"/>\r\n+ <fbc:geneProduct fbc:id="b4041" fbc:label="b4041" fbc:name="b4041" metaid="_94a9500a-9cb8-471a-960c-ed3dd82df137"/>\r\n+ <fbc:geneProduct fbc:id="b4040" fbc:label="b4040" fbc:name="b4040" metaid="_5f93eaf9-e592-4529-bb84-f8662'..b'tAssociation>\r\n+ <listOfReactants>\r\n+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1"/>\r\n+ </listOfReactants>\r\n+ <listOfProducts>\r\n+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_h_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_ggptrc_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>\r\n+ </listOfProducts>\r\n+ </reaction>\r\n+ <reaction fbc:lowerFluxBound="LOWER_BOUND_1000_0" fbc:upperFluxBound="UPPER_BOUND_1000_0" id="R_ARBtex" metaid="b50bec2f-a0bc-4dbb-af50-60907396df82" name="L-arabinose transport via diffusion (extracellular to periplasm)" reversible="true" sboTerm="SBO:0000185">\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="#b50bec2f-a0bc-4dbb-af50-60907396df82">\r\n+ <bqbiol:is>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR95913"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ARBtex"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:is>\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="b1377"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="b0929"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="b0241"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="b2215"/>\r\n+ </fbc:or>\r\n+ </fbc:geneProductAssociation>\r\n+ <listOfReactants>\r\n+ <speciesReference constant="true" species="M_arab__L_e" stoichiometry="1"/>\r\n+ </listOfReactants>\r\n+ <listOfProducts>\r\n+ <speciesReference constant="true" species="M_arab__L_p" 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_FACOAE120" metaid="_50a8274a-ed7a-4669-a5cf-95aa9824ac76" name="Fatty-acid-CoA thioesterase (dodecanoate)" reversible="false" sboTerm="SBO:0000176">\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="#_50a8274a-ed7a-4669-a5cf-95aa9824ac76">\r\n+ <bqbiol:is>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/ec-code/3.1.2.2"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR99128"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FACOAE120"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:is>\r\n+ </rdf:Description>\r\n+ </rdf:RDF>\r\n+ </annotation>\r\n+ <fbc:geneProductAssociation>\r\n+ <fbc:geneProductRef fbc:geneProduct="b0452"/>\r\n+ </fbc:geneProductAssociation>\r\n+ <listOfReactants>\r\n+ <speciesReference constant="true" species="M_ddcacoa_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1"/>\r\n+ </listOfReactants>\r\n+ <listOfProducts>\r\n+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_h_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>\r\n+ </listOfProducts>\r\n+ </reaction>\r\n+ </listOfReactions>\r\n+ </model>\r\n+</sbml>\r\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/CreateMetaNetwork/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/CreateMetaNetwork/test-data/Human-GEM_pathways.xml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 build/tools/DecomposeSBML/DecomposeSBML.xml --- a/build/tools/DecomposeSBML/DecomposeSBML.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,60 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_DecomposeSBML" name="DecomposeSBML" version="1.5.0"> - <description>Parse SBML to render list of composing entities: metabolites, reactions, genes and others.</description> - <xrefs> - <xref type="bio.tools">met4j</xref> - </xrefs> - <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.DecomposeSBML -i "$sbml" - $printMetabolites - $printReactions - $printCompartments - $printPathways - $printGenes - $noTypeCol - -o "$outputFile" -]]></command> - <inputs> - <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/> - <param argument="-m" checked="false" falsevalue="" label="Extract Metabolites" name="printMetabolites" truevalue="-m" type="boolean" value="false"/> - <param argument="-r" checked="false" falsevalue="" label="Extract Reactions" name="printReactions" truevalue="-r" type="boolean" value="false"/> - <param argument="-c" checked="false" falsevalue="" label="Extract Compartments" name="printCompartments" truevalue="-c" type="boolean" value="false"/> - <param argument="-p" checked="false" falsevalue="" label="Extract Pathways" name="printPathways" truevalue="-p" type="boolean" value="false"/> - <param argument="-g" checked="false" falsevalue="" label="Extract Genes" name="printGenes" truevalue="-g" type="boolean" value="false"/> - <param argument="-nt" checked="false" falsevalue="" label="Do not output type column" name="noTypeCol" truevalue="-nt" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="tsv" name="outputFile"/> - </outputs> - <tests> - <test> - <param name="sbml" value="Human-GEM_pathways.xml"/> - <output ftype="tsv" name="outputFile"> - <assert_contents> - <has_text_matching expression="GENE" n="86"/> - <has_text_matching expression="METABOLITE" n="111"/> - <has_text_matching expression="REACTION" n="75"/> - <has_text_matching expression="PATHWAY" n="3"/> - <has_text_matching expression="COMPARTMENT" n="5"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="Human-GEM_pathways.xml"/> - <param name="printReactions" value="true"/> - <param name="printMetabolites" value="true"/> - <param name="printGenes" value="true"/> - <param name="printCompartments" value="true"/> - <param name="noTypeCol" value="true"/> - <output ftype="tsv" name="outputFile"> - <assert_contents> - <has_n_lines n="277"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Parse SBML to render list of composing entities: metabolites, reactions, genes, pathways and compartments. The output file is a tsv with two columns, one with entities identifiers, and one with the entity type. If no entity type is selected, by default all of them are taken into account. Only identifiers are written, attributes can be extracted from dedicated apps or from the SBML2Tab.]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/DecomposeSBML/test-data/Human-GEM_pathways.xml --- a/build/tools/DecomposeSBML/test-data/Human-GEM_pathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,7661 +0,0 @@\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 1274e2a62479 -r 0976a6257300 build/tools/DegreeWeighting/DegreeWeighting.xml --- a/build/tools/DegreeWeighting/DegreeWeighting.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/DegreeWeighting/DegreeWeighting.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="develop"> <description>Provides tabulated compound graph edge list, with one column with target's degree.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DegreeWeighting#if str($pow): -pow "$pow" @@ -45,6 +45,8 @@ <data format="tsv" name="outputPath"/> </outputs> <tests/> - <help><![CDATA[Provides tabulated compound graph edge list, with one column with target's degree.Degree has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search. See Croes et al. 2006 (https://doi.org/10.1016/j.jmb.2005.09.079) and Croes et al. 2005 (https://doi.org/10.1093/nar/gki437)]]></help> - <citations/> + <help><![CDATA[Provides tabulated compound graph edge list, with one column with target's degree.Degree has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search.]]></help> + <citations> + <citation type="doi">10.1016/j.jmb.2005.09.079</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/DistanceMatrix/DistanceMatrix.xml --- a/build/tools/DistanceMatrix/DistanceMatrix.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/DistanceMatrix/DistanceMatrix.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="develop"> <description>Create a compound to compound distance matrix.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -34,30 +34,294 @@ </outputs> <tests> <test> + + + + + + + + + + + <param name="inputPath" value="toy_model.xml"/> + + + + + + + + + + + <output ftype="csv" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <has_n_lines n="9"/> + + + + + + + + + + + <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/> + + + + + + + + + + + <has_line_matching expression="B,1.0,Infinity,0.0,2.0,1.0,2.0,Infinity,Infinity" n="1"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> <test> + + + + + + + + + + + <param name="inputPath" value="toy_model.xml"/> + + + + + + + + + + + <param name="sideCompoundFile" value="sides.txt"/> + + + + + + + + + + + <param name="degree" value="true"/> + + + + + + + + + + + <param name="undirected" value="true"/> + + + + + + + + + + + <output ftype="csv" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <has_n_lines n="8"/> + + + + + + + + + + + <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/> + + + + + + + + + + + <has_line_matching expression="A,0.0,4.0,4.0,20.0,21.0,24.0,25.0" n="1"/> + + + + + + + + + + + <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/> + + + + + + + + + + + <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/> + + + + + + + + + + + <has_line_matching expression="D,8.0,4.0,4.0,0.0,1.0,4.0,5.0" n="1"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> <help><![CDATA[Create a compound to compound distance matrix. |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ExtractAnnotations/ExtractAnnotations.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/ExtractAnnotations/ExtractAnnotations.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,273 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="develop"> + <description>Extract databases' references from SBML annotations or notes.</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractAnnotations -i "$inputPath" + -export "$export" + -db "$db" + $uniq + $skip + -o "$outputPath" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-export" label="the type of entity to extract annotation, either metabolite, reaction, or gene" name="export" optional="false" type="select" value="METABOLITE"> + <option selected="true" value="METABOLITE">METABOLITE</option> + <option value="REACTION">REACTION</option> + <option value="GENE">GENE</option> + </param> + <param argument="-db" label="name of the referenced database to export annotations from, as listed in notes or identifiers.org base uri" name="db" optional="false" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-uniq" checked="false" falsevalue="" label="keep only one identifier if multiple are referenced for the same entity" name="uniq" truevalue="-uniq" type="boolean" value="false"/> + <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/> + </inputs> + <outputs> + <data format="tsv" name="outputPath"/> + </outputs> + <tests> + <test> + + + + + + + <param name="inputPath" value="Human-GEM_pathways.xml"/> + + + + + + + <param name="export" value="METABOLITE"/> + + + + + + + <param name="db" value="metanetx.chemical"/> + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="146"/> + + + + + + + <has_n_columns n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test> + + + + + + + <param name="inputPath" value="Human-GEM_pathways.xml"/> + + + + + + + <param name="export" value="METABOLITE"/> + + + + + + + <param name="db" value="metanetx.chemical"/> + + + + + + + <param name="skip" value="true"/> + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="145"/> + + + + + + + <has_n_columns n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test> + + + + + + + <param name="inputPath" value="Human-GEM_pathways.xml"/> + + + + + + + <param name="export" value="METABOLITE"/> + + + + + + + <param name="db" value="metanetx.chemical"/> + + + + + + + <param name="skip" value="true"/> + + + + + + + <param name="uniq" value="true"/> + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="111"/> + + + + + + + <has_n_columns n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ExtractAnnotations/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/ExtractAnnotations/test-data/Human-GEM_pathways.xml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 build/tools/ExtractPathways/ExtractPathways.xml --- a/build/tools/ExtractPathways/ExtractPathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ExtractPathways/ExtractPathways.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractPathways" name="ExtractPathways" version="1.5.0"> - <description>Extract pathway(s) from GSMN</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractPathways" name="ExtractPathways" version="develop"> + <description>Extract pathway(s) from a SBML file and create a sub-network SBML file</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath" -p "$pathwayId" @@ -24,17 +24,127 @@ </outputs> <tests> <test> + + + + + + + + + + + <param name="inputPath" value="XF_network.sbml"/> + + + + + + + + + + + <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/> + + + + + + + + + + + <output ftype="sbml" name="outputPath"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*<reaction.*" n="17"/> - <has_line_matching expression=".*groups:id=.*" n="2"/> - </assert_contents> - </output> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <is_valid_xml/> + + + + + + + + + + + + <has_line_matching expression=".*<reaction.*" n="17"/> + + + + + + + + + + + + <has_line_matching expression=".*groups:id=.*" n="2"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> - <help><![CDATA["Extract pathway(s) from GSMN: From a SBML file, Create a sub-network SBML file including only a selection of pathways]]></help> + <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file]]></help> <citations/> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ExtractSbmlAnnot/ExtractSbmlAnnot.xml --- a/build/tools/ExtractSbmlAnnot/ExtractSbmlAnnot.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,75 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="1.5.0"> - <description>Extract databases' references from SBML annotations or notes.</description> - <xrefs> - <xref type="bio.tools">met4j</xref> - </xrefs> - <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractSbmlAnnot -i "$inputPath" - -export "$export" - -db "$db" - $uniq - $skip - -o "$outputPath" -]]></command> - <inputs> - <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-export" label="the type of entity to extract annotation, either metabolite, reaction, or gene" name="export" optional="false" type="select" value="METABOLITE"> - <option selected="true" value="METABOLITE">METABOLITE</option> - <option value="REACTION">REACTION</option> - <option value="GENE">GENE</option> - </param> - <param argument="-db" label="name of the referenced database to export annotations from, as listed in notes or identifiers.org base uri" name="db" optional="false" type="text" value=""> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-uniq" checked="false" falsevalue="" label="keep only one identifier if multiple are referenced for the same entity" name="uniq" truevalue="-uniq" type="boolean" value="false"/> - <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="tsv" name="outputPath"/> - </outputs> - <tests> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="export" value="METABOLITE"/> - <param name="db" value="metanetx.chemical"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="146"/> - <has_n_columns n="2"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="export" value="METABOLITE"/> - <param name="db" value="metanetx.chemical"/> - <param name="skip" value="true"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="145"/> - <has_n_columns n="2"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="export" value="METABOLITE"/> - <param name="db" value="metanetx.chemical"/> - <param name="skip" value="true"/> - <param name="uniq" value="true"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="111"/> - <has_n_columns n="2"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ExtractSbmlAnnot/test-data/Human-GEM_pathways.xml --- a/build/tools/ExtractSbmlAnnot/test-data/Human-GEM_pathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,7661 +0,0 @@\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 1274e2a62479 -r 0976a6257300 build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml --- a/build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,17 +1,16 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="1.5.0"> - <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="develop"> + <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath" -s "$sourcePath" -t "$targetPath" $undirected - $asTable -sc "$sideCompoundFile" #if str($blkdReactionFile) != 'None': -br "$blkdReactionFile" @@ -23,14 +22,16 @@ -k "$k" #end if $st - -o "$outputPath" +#if str($format): + -f "$format" +#end if + -o "$output" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/> <param argument="-br" format="txt" label="a file containing list of blocked reactions to ignore" name="blkdReactionFile" optional="true" type="data" value=""/> <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/> @@ -40,26 +41,70 @@ </sanitizer> </param> <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="outputPath"/> + <data format="txt" name="output"/> </outputs> <tests> <test> - <param name="inputPath" value="toy_model.xml"/> - <param name="sourcePath" value="seeds.txt"/> - <param name="targetPath" value="targets.txt"/> - <param name="sideCompoundFile" value="sc.txt"/> - <output ftype="gml" name="outputPath"> - <assert_contents> - <has_line_matching expression=".*node.*" n="5"/> - <has_line_matching expression=".*edge.*" n="4"/> - </assert_contents> - </output> - </test> + + + + <param name="inputPath" value="toy_model.xml"/> + + + + <param name="sourcePath" value="seeds.txt"/> + + + + <param name="targetPath" value="targets.txt"/> + + + + <param name="sideCompoundFile" value="sc.txt"/> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + + <assert_contents> + + + + <has_line_matching expression=".*node.*" n="5"/> + + + + <has_line_matching expression=".*edge.*" n="4"/> + + + + </assert_contents> + + + + </output> + + + + </test> </tests> - <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. -The subnetwork corresponds to part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list. + <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. +The subnetwork corresponds to the part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list. Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.]]></help> <citations/> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ExtractSubNetwork/ExtractSubNetwork.xml --- a/build/tools/ExtractSubNetwork/ExtractSubNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ExtractSubNetwork/ExtractSubNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="1.5.0"> - <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="develop"> + <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath" -s "$sourcePath" @@ -19,12 +19,14 @@ #end if $chemicalSim $undirected - $asTable #if str($k): -k "$k" #end if $st - -o "$outputPath" +#if str($format): + -f "$format" +#end if + -o "$output" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> @@ -35,41 +37,82 @@ <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> <param argument="-sw" checked="false" falsevalue="" label="penalize traversal of non-relevant edges by using chemical similarity weighting" name="chemicalSim" truevalue="-sw" type="boolean" value="false"/> <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> </sanitizer> </param> <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="outputPath"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="inputPath" value="toy_model.xml"/> + + + <param name="sourcePath" value="seeds.txt"/> + + + <param name="targetPath" value="targets.txt"/> - <output ftype="gml" name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + <assert_contents> + + + <has_line_matching expression=".*node.*" n="3"/> + + + <has_line_matching expression=".*edge.*" n="2"/> + + + </assert_contents> + + + </output> + + + </test> </tests> - <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row. -The subnetwork correspond to part of the network that connects compounds from the first list to compounds from the second list. + <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row. +The subnetwork corresponds to the part of the network that connects compounds from the first list to compounds from the second list. Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting. -See previous works on subnetwork extraction for parameters recommendations:Frainay, C., & Jourdan, F. Computational methods to identify metabolic sub-networks based on metabolomic profiles. Bioinformatics 2016;1–14. https://doi.org/10.1093/bib/bbv115 -Faust, K., Croes, D., & van Helden, J. Prediction of metabolic pathways from genome-scale metabolic networks. Bio Systems 2011;105(2), 109–121. https://doi.org/10.1016/j.biosystems.2011.05.004 -Croes D, Couche F, Wodak SJ, et al. Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res 2005;33:W326–30. -Croes D, Couche F, Wodak SJ, et al. Inferring meaningful pathways in weighted metabolic networks. J Mol Biol 2006; 356:222–36. -Rahman SA, Advani P, Schunk R, et al. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics 2005;21:1189–93. -Pertusi DA, Stine AE, Broadbelt LJ, et al. Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics 2014;1–9. -McShan DC, Rao S, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics 2003;19:1692–8. -]]></help> - <citations/> +See previous works on subnetwork extraction for parameters recommendations.]]></help> + <citations> + <citation type="doi">10.1093/bib/bbv115</citation> + <citation type="doi">10.1016/j.biosystems.2011.05.004</citation> + <citation type="doi">10.1016/j.jmb.2005.09.079</citation> + <citation type="doi">10.1093/bioinformatics/btu760</citation> + <citation type="doi">10.1093/nar/gki437</citation> + <citation type="doi">10.1093/bioinformatics/bti116</citation> + <citation type="doi">10.1093/bioinformatics/btg217</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml --- a/build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,16 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.5.0"> - <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="develop"> + <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath" -s "$sourcePath" $undirected - $asTable -t "$targetPath" -sc "$sideCompoundFile" #if str($rExclude) != 'None': @@ -23,13 +22,15 @@ -k "$k" #end if $st - -o "$outputPath" +#if str($format): + -f "$format" +#end if + -o "$output" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/> <param argument="-re" format="txt" label="an optional file containing list of reactions to ignore" name="rExclude" optional="true" type="data" value=""/> @@ -40,26 +41,70 @@ </sanitizer> </param> <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="outputPath"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="inputPath" value="toy_model.xml"/> + + + <param name="sourcePath" value="seeds.txt"/> + + + <param name="targetPath" value="targets.txt"/> + + + <param name="sideCompoundFile" value="sides.txt"/> - <output ftype="gml" name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + <assert_contents> + + + <has_line_matching expression=".*node.*" n="3"/> + + + <has_line_matching expression=".*edge.*" n="2"/> + + + </assert_contents> + + + </output> + + + </test> </tests> - <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. -The subnetwork corresponds to part of the network that connects reactions from the first list to reactions from the second list. + <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. +The subnetwork corresponds to the part of the network that connects reactions from the first list to reactions from the second list. Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, reaction graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds to ignore for linking reactions must be provided. An optional edge weight file, if available, can also be used.]]></help> <citations/> </tool> |
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| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ExtractSubReactionNetwork/test-data/sides.txt --- a/build/tools/ExtractSubReactionNetwork/test-data/sides.txt Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ExtractSubReactionNetwork/test-data/sides.txt Fri Jan 31 18:28:53 2025 +0000 |
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| @@ -0,0 +1,14 @@ +// Copyright 2025 lcottret +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// https://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/FbcToNotes/FbcToNotes.xml --- a/build/tools/FbcToNotes/FbcToNotes.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/FbcToNotes/FbcToNotes.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,32 +1,122 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_FbcToNotes" name="FbcToNotes" version="1.5.0"> - <description>Convert FBC package annotations to sbml notes</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_FbcToNotes" name="FbcToNotes" version="develop"> + <description>Convert FBC package annotations to sbml html notes</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath" -o "$outputPath" ]]></command> <inputs> - <param argument="-i" format="sbml" label="input file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> </inputs> <outputs> <data format="sbml" name="outputPath"/> </outputs> <tests> <test> + + + + + + + + + + + <param name="inputPath" value="ECOL.xml"/> + + + + + + + + + + + <output ftype="sbml" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <is_valid_xml/> + + + + + + + + + + + <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> - <help><![CDATA[Convert FBC package annotations to sbml notes]]></help> - <citations/> + <help><![CDATA[Convert FBC package annotations to sbml html notes (see https://www.degruyter.com/document/doi/10.1515/jib-2017-0082/html)]]></help> + <citations> + <citation type="doi">10.1515/jib-2017-0082</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/GetBiggModelProteome/GetBiggModelProteome.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/GetBiggModelProteome/GetBiggModelProteome.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,79 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="develop"> + <description>Get proteome in fasta format of a model present in the BIGG database</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetBiggModelProteome -m "$modelId" + -o "$outputFile" +]]></command> + <inputs> + <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="fasta" name="outputFile"/> + </outputs> + <tests> + <test maxseconds="120"> + + + + + + + <param name="modelId" value="e_coli_core"/> + + + + + + + <output ftype="fasta" name="outputFile"> + + + + + + + <assert_contents> + + + + + + + <has_line_matching expression=".*name=.*" n="136"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help> + <citations> + <citation type="doi">10.1093/nar/gkv1049</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/GetEntities/GetEntities.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/GetEntities/GetEntities.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,198 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_GetEntities" name="GetEntities" version="develop"> + <description>Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetEntities -i "$sbml" + $printMetabolites + $printReactions + $printCompartments + $printPathways + $printGenes + $noTypeCol + -o "$outputFile" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-m" checked="false" falsevalue="" label="Extract Metabolites" name="printMetabolites" truevalue="-m" type="boolean" value="false"/> + <param argument="-r" checked="false" falsevalue="" label="Extract Reactions" name="printReactions" truevalue="-r" type="boolean" value="false"/> + <param argument="-c" checked="false" falsevalue="" label="Extract Compartments" name="printCompartments" truevalue="-c" type="boolean" value="false"/> + <param argument="-p" checked="false" falsevalue="" label="Extract Pathways" name="printPathways" truevalue="-p" type="boolean" value="false"/> + <param argument="-g" checked="false" falsevalue="" label="Extract Genes" name="printGenes" truevalue="-g" type="boolean" value="false"/> + <param argument="-nt" checked="false" falsevalue="" label="Do not write type column" name="noTypeCol" truevalue="-nt" type="boolean" value="false"/> + </inputs> + <outputs> + <data format="tsv" name="outputFile"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="Human-GEM_pathways.xml"/> + + + + + + + <output ftype="tsv" name="outputFile"> + + + + + + + <assert_contents> + + + + + + + <has_text_matching expression="GENE" n="86"/> + + + + + + + <has_text_matching expression="METABOLITE" n="111"/> + + + + + + + <has_text_matching expression="REACTION" n="75"/> + + + + + + + <has_text_matching expression="PATHWAY" n="3"/> + + + + + + + <has_text_matching expression="COMPARTMENT" n="5"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test> + + + + + + + <param name="sbml" value="Human-GEM_pathways.xml"/> + + + + + + + <param name="printReactions" value="true"/> + + + + + + + <param name="printMetabolites" value="true"/> + + + + + + + <param name="printGenes" value="true"/> + + + + + + + <param name="printCompartments" value="true"/> + + + + + + + <param name="noTypeCol" value="true"/> + + + + + + + <output ftype="tsv" name="outputFile"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="277"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.The output file is a tabulated file with two columns, one with entity identifiers, and one with the entity type. If no entity type is selected, all of them are returned by default. Only identifiers are written, attributes can be extracted from dedicated apps or from the Sbml2Tab app.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/GetEntities/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/GetEntities/test-data/Human-GEM_pathways.xml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 build/tools/GetGenesFromReactions/GetGenesFromReactions.xml --- a/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.5.0"> - <description>Get gene lists from a list of reactions and a GSMN.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="develop"> + <description>Get gene lists from a list of reactions and 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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml" -r "$reactionFile" @@ -34,17 +34,127 @@ </outputs> <tests> <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="reactionFile" value="XF_network_R_Seed.tab"/> - <output ftype="tsv" name="outputFile"> - <assert_contents> - <has_n_lines n="2"/> - <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> - <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> - </assert_contents> - </output> - </test> + + + + + + + + + + + + <param name="sbml" value="XF_network.sbml"/> + + + + + + + + + + + + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + + + + + + + + + + + + <output ftype="tsv" name="outputFile"> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <has_n_lines n="2"/> + + + + + + + + + + + + <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> + + + + + + + + + + + + <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + + </test> </tests> - <help><![CDATA[Get associated gene list from a list of reactions and a GSMN. Parse GSMN GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help> + <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help> <citations/> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,94 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetMetaboliteAttributes -i "$sbml" + -o "$outputFile" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/> + </inputs> + <outputs> + <data format="tsv" name="outputFile"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <output ftype="tsv" name="outputFile"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="9"/> + + + + + + + <has_n_columns n="6"/> + + + + + + + <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/> + + + + + + + <has_line_matching expression=".*C.*NC.*" n="1"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/GetMetaboliteAttributes/test-data/tests.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/GetMetaboliteAttributes/test-data/tests.tsv Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,9 @@ +id name formula charge smiles inchi +A A null 0 null null +B B null 0 null null +A_ext A_ext null 0 C[C@@H](C(=O)O)NC 1S/C2H6O/c1-2-3/h3H,2H2,1H3 +C C null 0 null null +D D null 0 null null +E E null 0 null null +D_ext D_ext null 0 null null +E_ext E_ext null 0 null null |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/GetMetaboliteAttributes/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/GetMetaboliteAttributes/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/GetModelProteome/GetModelProteome.xml --- a/build/tools/GetModelProteome/GetModelProteome.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,35 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_GetModelProteome" name="GetModelProteome" version="1.5.0"> - <description>Get proteome in fasta format of a model present in BIGG</description> - <xrefs> - <xref type="bio.tools">met4j</xref> - </xrefs> - <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetModelProteome -m "$modelId" - -o "$outputFile" -]]></command> - <inputs> - <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="fasta" name="outputFile"/> - </outputs> - <tests> - <test maxseconds="120"> - <param name="modelId" value="e_coli_core"/> - <output ftype="fasta" name="outputFile"> - <assert_contents> - <has_line_matching expression=".*name=.*" n="136"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Get proteome in fasta format of a model present in BIGG]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/GetModelProteome/proteome.fas --- a/build/tools/GetModelProteome/proteome.fas Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1153 +0,0 @@\n->b0755 name=gpmA\n-MAVTKLVLVRHGESQWNKENRFTGWYDVDLSEKGVSEAKAAGKLLKEEGYSFDFAYTSVL\n-KRAIHTLWNVLDELDQAWLPVEKSWKLNERHYGALQGLNKAETAEKYGDEQVKQWRRGFA\n-VTPPELTKDDERYPGHDPRYAKLSEKELPLTESLALTIDRVIPYWNETILPRMKSGERVI\n-IAAHGNSLRALVKYLDNMSEEEILELNIPTGVPLVYEFDENFKPLKRYYLGNADEIAAKA\n-AAVANQGKAK\n->b0008 name=talB\n-MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRKLIDDAVAWAK\n-QQSNDRAQQIVDATDKLAVNIGLEILKLVPGRISTEVDARLSYDTEASIAKAKRLIKLYN\n-DAGISNDRILIKLASTWQGIRAAEQLEKEGINCNLTLLFSFAQARACAEAGVFLISPFVG\n-RILDWYKANTDKKEYAPAEDPGVVSVSEIYQYYKEHGYETVVMGASFRNIGEILELAGCD\n-RLTIAPALLKELAESEGAIERKLSYTGEVKARPARITESEFLWQHNQDPMAVDKLAEGIR\n-KFAIDQEKLEKMIGDLL\n->b3951 name=pflD\n-MTNRISRLKTALFANTREISLERALLYTASHRQTEGEPVILRRAKATAYILEHVEISIRD\n-EELIAGNRTVKPRAGIMSPEMDPYWLLKELDQFPTRPQDRFAISEEDKRIYREELFPYWE\n-KRSMKDFINGQMTDEVKAATNTQIFSINQTDKGQGHIIIDYPRLLNHGLGELVAQMQQHC\n-QQQPENHFYQAALLLLEASQKHILRYAELAETMAANCTDAQRREELLTIAEISRHNAQHK\n-PQTFWQACQLFWYMNIILQYESNASSLSLGRFDQYMLPFYQTSLTQGEDAAFLKELLESL\n-WVKCNDIVLLRSTSSARYFAGFPTGYTALLGGLTENGRSAVNVLSFLCLDAYQSVQLPQP\n-NLGVRTNALIDTPFLMKTAETIRFGTGIPQIFNDEVVVPAFLNRGVSLEDARDYSVVGCV\n-ELSIPGRTYGLHDIAMFNLLKVMEICLHENEGNAALTYEGLLEQIRAKISHYITLMVEGS\n-NICDIGHRDWAPVPLLSSFISDCLEKGRDITDGGARYNFSGVQGIGIANLSDSLHALKGM\n-VFEQQRLSFDELLSVLKANFATPEGEKVRARLINRFEKYGNDIDEVDNISAELLRHYCKE\n-VEKYQNPRGGYFTPGSYTVSAHVPLGSVVGATPDGRFAGEQLADGGLSPMLGQDAQGPTA\n-VLKSVSKLDNTLLSNGTLLNVKFTPATLEGEAGLRKLADFLRAFTQLKLQHIQFNVVNAD\n-TLREAQQRPQDYAGLVVRVAGYSAFFVELSKEIQDDIIRRTAHQL\n->b0723 name=sdhA\n-MKLPVREFDAVVIGAGGAGMRAALQISQSGQTCALLSKVFPTRSHTVSAQGGITVALGNT\n-HEDNWEWHMYDTVKGSDYIGDQDAIEYMCKTGPEAILELEHMGLPFSRLDDGRIYQRPFG\n-GQSKNFGGEQAARTAAAADRTGHALLHTLYQQNLKNHTTIFSEWYALDLVKNQDGAVVGC\n-TALCIETGEVVYFKARATVLATGGAGRIYQSTTNAHINTGDGVGMAIRAGVPVQDMEMWQ\n-FHPTGIAGAGVLVTEGCRGEGGYLLNKHGERFMERYAPNAKDLAGRDVVARSIMIEIREG\n-RGCDGPWGPHAKLKLDHLGKEVLESRLPGILELSRTFAHVDPVKEPIPVIPTCHYMMGGI\n-PTKVTGQALTVNEKGEDVVVPGLFAVGEIACVSVHGANRLGGNSLLDLVVFGRAAGLHLQ\n-ESIAEQGALRDASESDVEASLDRLNRWNNNRNGEDPVAIRKALQECMQHNFSVFREGDAM\n-AKGLEQLKVIRERLKNARLDDTSSEFNTQRVECLELDNLMETAYATAVSANFRTESRGAH\n-SRFDFPDRDDENWLCHSLYLPESESMTRRSVNMEPKLRPAFPPKIRTY\n->b1723 name=pfkB\n-MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFP\n-AGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQ\n-LEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGN\n-IELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQ\n-VVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDT\n-QKIYAYLSR\n->b3603 name=lldP\n-MNLWQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKM\n-PVANALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLI\n-VGFCFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVA\n-GQVTGIDSFEIGQMVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYL\n-SSNFIGPELPDIISSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVL\n-RAWTPFLFLTATVTLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAY\n-AAVFKFDWFSATGTAILFAALLSIVWLKMKPSDAISTFGSTLKELALPIYSIGMVLAFAF\n-ISNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGV\n-SDLLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCIVGVITT\n-LQAYVLTWMIP\n->b1818 name=manY\n-MEITTLQIVLVFIVACIAGMGSILDEFQFHRPLIACTLVGIVLGDMKTGIIIGGTLEMIA\n-LGWMNIGAAVAPDAALASIISTILVIAGHQSIGAGIALAIPLAAAGQVLTIIVRTITVAF\n-QHAADKAADNGNLTAISWIHVSSLFLQAMRVAIPAVIVALSVGTSEVQNMLNAIPEVVTN\n-GLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFTNFNLVALGVIGTVMAVLYIQ\n-LSPKYNRVAGAPAQAAGNNDLDNELD\n->b0722 name=sdhD\n-MVSNASALGRNGVHDFILVRATAIVLTLYIIYMVGFFATSGELTYEVWIGFFASAFTKVF\n-TLLALFSILIHAWIGMWQVLTDYVKPLALRLMLQLVIVVALVVYVIYGFVVVWGV\n->b3731 name=atpC\n-MAMTYHLDVVSAEQQMFSGLVEKIQVTGSEGELGIYPGHAPLLTAIKPGMIRIVKQHGHE\n-EFIYLSGGILEVQPGNVTVLADTAIRGQDLDEARAMEAKRKAEEHISSSHGDVDYAQASA\n-ELAKAIAQLRVIELTKKAM\n->b2280 name=nuoJ\n-MEFAFYICGLIAILATLRVITHTNPVHALLYLIISLLAISGVFFSLGAYFAGALEIIVYA\n-GAIMVLFVFVVMMLNLGGSEIEQERQWLKPQVWIGPAILSAIMLVVIVYAILGVNDQGID\n-GTPISAKAVGITLFGPYVLAVELASMLLLAGLVVAFHVGREERAGEVLSNRKDDSAKRKT\n-EEHA\n->b0767 name=pgl\n-MKQTVYIASPESQQIHVWNLNHEGALTLTQVVDVPGQVQPMVVSPDKRYLYVGVRPEFRV\n-LAYRIAPDDGALTFAAESALPGSPTHISTDHQGQFVFVGSYNAGNVSVTRLEDGLPVGVV\n-DVVEGLDGCHSANISPDNRTLWVPALKQDRICLFTVSDDGHLVAQD'..b'AETKDGRWYPEFFRINFSRCIFCGLCEEACPTTAIQLTPDF\n-EMGEYKRQDLVYEKEDLLISGPGKYPEYNFYRMAGMAIDGKDKGEAENEAKPIDVKSLLP\n->b4301 name=sgcE\n-MILHPSLASANPLHYGRELTALDNLDFGSLHLDIEDSSFINNITFGMKTVQAVARQTPHP\n-LSFHFMLARPQRWFNALAEIRPAWIFVHAETLDYPSETLTEIRHTGARAGLVFNPATPID\n-AWRYLASELDGVMVMTSEPDGQGQRFIPSMCEKIQKVRTAFPQTECWADGGITLAAAQQL\n-AAAGAQHMVIGRALFSSSDYRATLAQFATL\n->b2463 name=maeB\n-MDDQLKQSALDFHEFPVPGKIQVSPTKPLATQRDLALAYSPGVAAPCLEIEKDPLKAYKY\n-TARGNLVAVISNGTAVLGLGNIGALAGKPVMEGKGVLFKKFAGIDVFDIEVDELDPDKFI\n-EVVAALEPTFGGINLEDIKAPECFYIEQKLRERMNIPVFHDDQHGTAIISTAAILNGLRV\n-VEKNISDVRMVVSGAGAAAIACMNLLVALGLQKHNIVVCDSKGVIYQGREPNMAETKAAY\n-AVVDDGKRTLDDVIEGADIFLGCSGPKVLTQEMVKKMARAPMILALANPEPEILPPLAKE\n-VRPDAIICTGRSDYPNQVNNVLCFPFIFRGALDVGATAINEEMKLAAVRAIAELAHAEQS\n-EVVASAYGDQDLSFGPEYIIPKPFDPRLIVKIAPAVAKAAMESGVATRPIADFDVYIDKL\n-TEFVYKTNLFMKPIFSQARKAPKRVVLPEGEEARVLHATQELVTLGLAKPILIGRPNVIE\n-MRIQKLGLQIKAGVDFEIVNNESDPRFKEYWTEYFQIMKRRGVTQEQAQRALISNPTVIG\n-AIMVQRGEADAMICGTVGDYHEHFSVVKNVFGYRDGVHTAGAMNALLLPSGNTFIADTYV\n-NDEPDAEELAEITLMAAETVRRFGIEPRVALLSHSNFGSSDCPSSSKMRQALELVRERAP\n-ELMIDGEMHGDAALVEAIRNDRMPDSSLKGSANILVMPNMEAARISYNLLRVSSSEGVTV\n-GPVLMGVAKPVHVLTPIASVRRIVNMVALAVVEAQTQPL\n->b2133 name=dld\n-MSSMTTTDNKAFLNELARLVGSSHLLTDPAKTARYRKGFRSGQGDALAVVFPGSLLELWR\n-VLKACVTADKIILMQAANTGLTEGSTPNGNDYDRDVVIISTLRLDKLHVLGKGEQVLAYP\n-GTTLYSLEKALKPLGREPHSVIGSSCIGASVIGGICNNSGGSLVQRGPAYTEMSLFARIN\n-EDGKLTLVNHLGIDLGETPEQILSKLDDDRIKDDDVRHDGRHAHDYDYVHRVRDIEADTP\n-ARYNADPDRLFESSGCAGKLAVFAVRLDTFEAEKNQQVFYIGTNQPEVLTEIRRHILANF\n-ENLPVAGEYMHRDIYDIAEKYGKDTFLMIDKLGTDKMPFFFNLKGRTDAMLEKVKFFRPH\n-FTDRAMQKFGHLFPSHLPPRMKNWRDKYEHHLLLKMAGDGVGEAKSWLVDYFKQAEGDFF\n-VCTPEEGSKAFLHRFAAAGAAIRYQAVHSDEVEDILALDIALRRNDTEWYEHLPPEIDSQ\n-LVHKLYYGHFMCYVFHQDYIVKKGVDVHALKEQMLELLQQRGAQYPAEHNVGHLYKAPET\n-LQKFYRENDPTNSMNPGIGKTSKRKNWQEVE\n->b3612 name=gpmM\n-MLVSKKPMVLVILDGYGYREEQQDNAIFSAKTPVMDALWANRPHTLIDASGLEVGLPDRQ\n-MGNSEVGHVNLGAGRIVYQDLTRLDVEIKDRAFFANPVLTGAVDKAKNAGKAVHIMGLLS\n-AGGVHSHEDHIMAMVELAAERGAEKIYLHAFLDGRDTPPRSAESSLKKFEEKFAALGKGR\n-VASIIGRYYAMDRDNRWDRVEKAYDLLTLAQGEFQADTAVAGLQAAYARDENDEFVKATV\n-IRAEGQPDAAMEDGDALIFMNFRADRAREITRAFVNADFDGFARKKVVNVDFVMLTEYAA\n-DIKTAVAYPPASLVNTFGEWMAKNDKTQLRISETEKYAHVTFFFNGGVEESFKGEDRILI\n-NSPKVATYDLQPEMSSAELTEKLVAAIKSGKYDTIICNYPNGDMVGHTGVMEAAVKAVEA\n-LDHCVEEVAKAVESVGGQLLITADHGNAEQMRDPATGQAHTAHTNLPVPLIYVGDKNVKA\n-VEGGKLSDIAPTMLSLMGMEIPQEMTGKPLFIVE\n->b2287 name=nuoB\n-MDYTLTRIDPNGENDRYPLQKQEIVTDPLEQEVNKNVFMGKLNDMVNWGRKNSIWPYNFG\n-LSCCYVEMVTSFTAVHDVARFGAEVLRASPRQADLMVVAGTCFTKMAPVIQRLYDQMLEP\n-KWVISMGACANSGGMYDIYSVVQGVDKFIPVDVYIPGCPPRPEAYMQALMLLQESIGKER\n-RPLSWVVGDQGVYRANMQSERERKRGERIAVTNLRTPDEI\n->b3737 name=atpE\n-MENLNMDLLYMAAAVMMGLAAIGAAIGIGILGGKFLEGAARQPDLIPLLRTQFFIVMGLV\n-DAIPMIAVGLGLYVMFAVA\n->b0810 name=glnP\n-MQFDWSAIWPAIPLLIEGAKMTLWISVLGLAGGLVIGLLAGFARTFGGWIANHVALVFIE\n-VIRGTPIVVQVMFIYFALPMAFNDLRIDPFTAAVVTIMINSGAYIAEITRGAVLSIHKGF\n-REAGLALGLSRWETIRYVILPLALRRMLPPLGNQWIISIKDTSLFIVIGVAELTRQGQEI\n-IAGNFRALEIWSAVAVFYLIITLVLSFILRRLERRMKIL\n->b0356 name=frmA\n-MKSRAAVAFAPGKPLEIVEIDVAPPKKGEVLIKVTHTGVCHTDAFTLSGDDPEGVFPVVL\n-GHEGAGVVVEVGEGVTSVKPGDHVIPLYTAECGECEFCRSGKTNLCVAVRETQGKGLMPD\n-GTTRFSYNGQPLYHYMGCSTFSEYTVVAEVSLAKINPEANHEHVCLLGCGVTTGIGAVHN\n-TAKVQPGDSVAVFGLGAIGLAVVQGARQAKAGRIIAIDTNPKKFDLARRFGATDCINPND\n-YDKPIKDVLLDINKWGIDHTFECIGNVNVMRAALESAHRGWGQSVIIGVAVAGQEISTRP\n-FQLVTGRVWKGSAFGGVKGRSQLPGMVEDAMKGDIDLEPFVTHTMSLDEINDAFDLMHEG\n-KSIRTVIRY\n->b2935 name=tktA\n-MSSRKELANAIRALSMDAVQKAKSGHPGAPMGMADIAEVLWRDFLKHNPQNPSWADRDRF\n-VLSNGHGSMLIYSLLHLTGYDLPMEELKNFRQLHSKTPGHPEVGYTAGVETTTGPLGQGI\n-ANAVGMAIAEKTLAAQFNRPGHDIVDHYTYAFMGDGCMMEGISHEVCSLAGTLKLGKLIA\n-FYDDNGISIDGHVEGWFTDDTAMRFEAYGWHVIRDIDGHDAASIKRAVEEARAVTDKPSL\n-LMCKTIIGFGSPNKAGTHDSHGAPLGDAEIALTREQLGWKYAPFEIPSEIYAQWDAKEAG\n-QAKESAWNEKFAAYAKAYPQEAAEFTRRMKGEMPSDFDAKAKEFIAKLQANPAKIASRKA\n-SQNAIEAFGPLLPEFLGGSADLAPSNLTLWSGSKAINEDAAGNYIHYGVREFGMTAIANG\n-ISLHGGFLPYTSTFLMFVEYARNAVRMAALMKQRQVMVYTHDSIGLGEDGPTHQPVEQVA\n-SLRVTPNMSTWRPCDQVESAVAWKYGVERQDGPTALILSRQNLAQQERTEEQLANIARGG\n-YVLKDCAGQPELIFIATGSEVELAVAAYEKLTAEGVKARVVSMPSTDAFDKQDAAYRESV\n-LPKAVTARVAVEAGIADYWYKYVGLNGAIVGMTTFGESAPAELLFEEFGFTVDNVVAKAK\n-ELL\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml --- a/build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="1.5.0">\n- <description>Get reactants lists from a list of reactions and a GSMN.</description>\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="develop">\n+ <description>Get reactant lists from a list of reactions and a SBML file.</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetReactantsFromReactions -i "$sbml"\n -r "$reactionFile"\n@@ -38,38 +38,357 @@\n </outputs>\n <tests>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="sbml" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="reactionFile" value="XF_network_R_Seed.tab"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="tsv" name="outputFile">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_GLUN" n="4"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_ACGS" n="5"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="sbml" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="reactionFile" value="XF_network_R_Seed.tab"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="printSubstrates" value="true"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="tsv" name="outputFile">\n+ '..b' \n+ \n <has_text_matching expression="R_GLUN" n="2"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_ACGS" n="5"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="sbml" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="reactionFile" value="XF_network_R_Seed.tab"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="printProducts" value="true"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="tsv" name="outputFile">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_GLUN" n="2"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_ACGS" n="5"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n- <help><![CDATA[Get reactants lists from a list of reactions and a GSMN. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered both substrates and products]]></help>\n+ <help><![CDATA[Get reactant lists from a list of reactions and a Sbml file. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered as both substrates and products]]></help>\n <citations/>\n </tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/Kegg2Sbml/Kegg2Sbml.xml --- a/build/tools/Kegg2Sbml/Kegg2Sbml.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/Kegg2Sbml/Kegg2Sbml.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,16 +1,16 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="develop"> <description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org): -org "$org" #end if - -sbml "$sbml" + -o "$sbml" ]]></command> <inputs> <param argument="-org" label="[] Kegg org id. Must be 3 letters (" name="org" optional="true" type="text" value=""> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/LoadPoint/LoadPoint.xml --- a/build/tools/LoadPoint/LoadPoint.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/LoadPoint/LoadPoint.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_LoadPoint" name="LoadPoint" version="1.5.0"> - <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug target.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_LoadPoint" name="LoadPoint" version="develop"> + <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -30,16 +30,104 @@ </outputs> <tests> <test> + + + + + + + + + + + <param name="inputPath" value="toy_model.xml"/> + + + + + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <has_n_columns n="3"/> + + + + + + + + + + + <has_n_lines n="8"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> - <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug target. + <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. From Rahman et al. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinf. (2006): For a given metabolic network, the load L on metabolite m can be defined as : ln [(pm/km)/(∑Mi=1Pi)/(∑Mi=1Ki)] @@ -48,5 +136,7 @@ P is the total number of shortest paths; K is the sum of links in the metabolic network of M metabolites (where M is the number of metabolites in the network). Use of the logarithm makes the relevant values more distinguishable.]]></help> - <citations/> + <citations> + <citation type="doi">10.1093/bioinformatics/btl181</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/MetaboRank/MetaboRank.xml --- a/build/tools/MetaboRank/MetaboRank.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/MetaboRank/MetaboRank.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_MetaboRank" name="MetaboRank" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_MetaboRank" name="MetaboRank" version="develop"> <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath" -s "$seedsFilePath" @@ -44,15 +44,125 @@ </outputs> <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> + + + + + + + + + + + + <has_n_lines n="1100"/> + + + + + + + + + + + + <has_n_columns n="11"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network. @@ -60,6 +170,8 @@ The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining. It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks. For convenience, a one dimensional centrality rank is also computed from the highest rank from PageRank or CheiRank, and using lowest rank as tie-breaker. -See publication for more information: Frainay et al. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results, Bioinformatics (35-2), https://doi.org/10.1093/bioinformatics/bty577]]></help> - <citations/> +See publication for more information.]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/bty577</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/NameMatcher/NameMatcher.xml --- a/build/tools/NameMatcher/NameMatcher.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/NameMatcher/NameMatcher.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_NameMatcher" name="NameMatcher" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_NameMatcher" name="NameMatcher" version="develop"> <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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.NameMatcher#if str($n): -nMatch "$n" @@ -16,7 +16,7 @@ #if str($col): -col "$col" #end if - -sbml "$sbml" + -i "$sbml" -compound "$input" #if str($comment): -c "$comment" @@ -27,7 +27,7 @@ -o "$outputFile" ]]></command> <inputs> - <param argument="-nMatch" label="[1] Number of match to return per name" name="n" optional="true" type="text" value="1"> + <param argument="-nMatch" label="[1] Number of matchs to return per name" name="n" optional="true" type="text" value="1"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> </sanitizer> @@ -42,7 +42,7 @@ <valid initial="string.printable"/> </sanitizer> </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> + <param argument="-i" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> <param argument="-compound" format="tsv" label="Compound file containing one column with compound names to search among the SBML entries" name="input" optional="false" type="data" value=""/> <param argument="-c" label="[#] Comment String in the compound file. The lines beginning by this string won't be read" name="comment" optional="true" type="text" value="#"> <sanitizer invalid_char="_"> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/NetworkSummary/NetworkSummary.xml --- a/build/tools/NetworkSummary/NetworkSummary.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/NetworkSummary/NetworkSummary.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.5.0"> - <description>Create a report summarizing several graph measures characterising the structure of the network.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_NetworkSummary" name="NetworkSummary" version="develop"> + <description>Create a report summarizing several graph measures characterising the structure 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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -26,14 +26,92 @@ </outputs> <tests> <test> - <param name="inputPath" value="toy_model.xml"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines min="1"/> - </assert_contents> - </output> - </test> + + + + + + + + + + + + <param name="inputPath" value="toy_model.xml"/> + + + + + + + + + + + + <output name="outputPath"> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <has_n_lines min="1"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + + </test> </tests> - <help><![CDATA[Use a metabolic network in SBML file and an optional list of side compounds, and produce a report summarizing several graph measures characterising the structure of the network.This includes (non-exhaustive list): size and order, connectivity, density, degree distribution, shortest paths length, top centrality nodes...]]></help> + <help><![CDATA[Create a report summarizing several graph measures characterising the structure of a metabolic network. +Use a metabolic network in SBML file and an optional list of side compounds, and produce a report summarizing several graph measures characterising the structure of the network.This includes (non-exhaustive list): size and order, connectivity, density, degree distribution, shortest paths length, top centrality nodes...]]></help> <citations/> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ORApathwayEnrichment/ORApathwayEnrichment.xml --- a/build/tools/ORApathwayEnrichment/ORApathwayEnrichment.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ORApathwayEnrichment/ORApathwayEnrichment.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,12 +1,286 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="1.5.0">\n- <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.\n-The fisher exact test compute the probability p to randomly get the given set of value. \n-This version compute the probability to get at least the given overlap between the given set and the given modality :\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="develop">\n+ <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.</description>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != \'nan\':\n+ -th "$th"\n+#end if\n+ -i "$sbml"\n+ -d "$input"\n+#if str($corr):\n+ -c "$corr"\n+#end if\n+ -o "$outputFile"\n+]]></command>\n+ <inputs>\n+ <param argument="-th" label="threshold to select significant pathways. No filtering if <=0" name="th" optional="true" type="float" value="0.0"/>\n+ <param argument="-i" format="sbml" label="Input model : SBML file with pathway annotation" name="sbml" optional="false" type="data" value=""/>\n+ <param argument="-d" format="tsv" label="Input data : Compounds of interest file, as one SBML specie identifier per line" name="input" optional="false" type="data" value=""/>\n+ <param argument="-c" label="Method for multiple testing p-value adjustment." name="corr" optional="true" type="select" value="BenjaminiHochberg">\n+ <option value="Bonferroni">Bonferroni</option>\n+ <option selected="true" value="BenjaminiHochberg">BenjaminiHochberg</option>\n+ <option value="HolmBonferroni">HolmBonferroni</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data format="tsv" name="outputFile"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <param name="input" value="XF_network_C_NOI.txt"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <output name="outputFile">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <has_n_columns n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <has_n_lines n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ '..b'\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <has_n_lines n="2"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.\n+The fisher exact test computes the probability p to randomly get the given set of values. \n+This version computes the probability to get at least the given overlap between the given set and the given modality :\n Sum the hypergeometric probability with increasing target/query intersection cardinality.\n \n The hypergeometric probability is computed from the following contingency table entries.\n-(value in cells correspond to the marginal totals of each intersection groups)\n+(values in cells correspond to the marginal totals of each intersection groups)\n \t\t\t\tQuery\t!Query\n \tTarget\t\ta\t\tb\n \t!Target\t\tc\t\td\n@@ -18,60 +292,6 @@\n - Bonferroni: adjusted p-value = p*n\n - Benjamini-Hochberg: adjusted p-value = p*n/k\n - Holm-Bonferroni: adjusted p-value = p*(n+1-k)\n-n : number of tests; k : pvalue rank</description>\n- <xrefs>\n- <xref type="bio.tools">met4j</xref>\n- </xrefs>\n- <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>\n- </requirements>\n- <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != \'nan\':\n- -th "$th"\n-#end if\n- -s "$sbml"\n- -i "$input"\n-#if str($corr):\n- -c "$corr"\n-#end if\n- -o "$outputFile"\n-]]></command>\n- <inputs>\n- <param argument="-th" label="threshold to select significant pathways. No filtering if <=0" name="th" optional="true" type="float" value="0.0"/>\n- <param argument="-s" format="sbml" label="Input model : SBML file with pathway annotation" name="sbml" optional="false" type="data" value=""/>\n- <param argument="-i" format="tsv" label="Input data : Compounds of interest file, as one SBML specie identifier per line" name="input" optional="false" type="data" value=""/>\n- <param argument="-c" label="Method for multiple testing p-value adjustment." name="corr" optional="true" type="select" value="BenjaminiHochberg">\n- <option value="Bonferroni">Bonferroni</option>\n- <option selected="true" value="BenjaminiHochberg">BenjaminiHochberg</option>\n- <option value="HolmBonferroni">HolmBonferroni</option>\n- </param>\n- </inputs>\n- <outputs>\n- <data format="tsv" name="outputFile"/>\n- </outputs>\n- <tests>\n- <test>\n- <param name="sbml" value="XF_network.sbml"/>\n- <param name="input" value="XF_network_C_NOI.txt"/>\n- <output name="outputFile">\n- <assert_contents>\n- <has_n_columns n="3"/>\n- <has_n_lines n="3"/>\n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="sbml" value="XF_network.sbml"/>\n- <param name="input" value="XF_network_C_NOI.txt"/>\n- <param name="corr" value="HolmBonferroni"/>\n- <param name="th" value="0.005"/>\n- <output name="outputFile">\n- <assert_contents>\n- <has_n_columns n="3"/>\n- <has_n_lines n="2"/>\n- </assert_contents>\n- </output>\n- </test>\n- </tests>\n- <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.]]></help>\n+n : number of tests; k : pvalue rank]]></help>\n <citations/>\n </tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/PathwayNet/PathwayNet.xml --- a/build/tools/PathwayNet/PathwayNet.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,38 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_PathwayNet" name="PathwayNet" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PathwayNet -s "$inputPath" -#if str($inputSide) != 'None': - -sc "$inputSide" -#end if - $removeIsolated - $onlySourcesAndSinks -#if str($weightFile) != 'None': - -cw "$weightFile" -#end if - $connectors - $asMatrix - -o "$outputPath" -]]></command> - <inputs> - <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-sc" format="txt" label="input Side compound file (recommended)" name="inputSide" optional="true" type="data" value=""/> - <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> - <param argument="-oss" checked="false" falsevalue="" label="consider only metabolites that are source or sink in the pathway (i.e non-intermediary compounds)" name="onlySourcesAndSinks" truevalue="-oss" type="boolean" value="false"/> - <param argument="-cw" format="tsv" label="an optional file containing weights for pathway pairs" name="weightFile" optional="true" type="data" value=""/> - <param argument="-ncw" checked="false" falsevalue="" label="set number of connecting compounds as weight" name="connectors" truevalue="-ncw" type="boolean" value="false"/> - <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="gml" name="outputPath"/> - </outputs> - <tests/> - <help><![CDATA[Genome-scale metabolic networks are often partitioned into metabolic pathways. Pathways are frequently considered independently despite frequent coupling in their activity due to shared metabolites. In order to decipher the interconnections linking overlapping pathways, this app proposes the creation of "Pathway Network", where two pathways are linked if they share compounds.]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/PrecursorNetwork/PrecursorNetwork.xml --- a/build/tools/PrecursorNetwork/PrecursorNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/PrecursorNetwork/PrecursorNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="develop"> <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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" -t "$targetsFilePath" @@ -15,7 +15,9 @@ #if str($reactionToIgnoreFile) != 'None': -ir "$reactionToIgnoreFile" #end if - $asTable +#if str($format): + -f "$format" +#end if -o "$output" ]]></command> <inputs> @@ -23,21 +25,58 @@ <param argument="-t" format="txt" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/> <param argument="-sc" format="txt" label="an optional file containing list of ubiquitous compounds to be considered already available" name="sideCompoundFile" optional="true" type="data" value=""/> <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope)" name="reactionToIgnoreFile" optional="true" type="data" value=""/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="output"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="sbmlFilePath" value="toy_model.xml"/> + + + <param name="targetsFilePath" value="targets.txt"/> - <output ftype="gml" name="output"> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + <assert_contents> + + + <has_line_matching expression=".*node.*" n="13"/> + + + <has_line_matching expression=".*edge.*" n="15"/> + + + </assert_contents> + + + </output> + + + </test> </tests> <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml --- a/build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="1.5.0">\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="develop">\n <description>Create a reaction to reaction distance matrix.</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath"\n #if str($sideCompoundFile) != \'None\':\n@@ -38,91 +38,982 @@\n </outputs>\n <tests>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputPath" value="toy_model.xml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="csv" name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="8"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputPath" value="toy_model.xml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="undirected" value="true"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ '..b'\n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputPath" value="toy_model.xml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="sideCompoundFile" value="sides.txt"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="rExclude" value="rexclude.txt"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="csv" name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="6"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n <help><![CDATA[Create a reaction to reaction distance matrix.\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SBMLwizard/SBMLwizard.xml --- a/build/tools/SBMLwizard/SBMLwizard.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,79 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SBMLwizard" name="SBMLwizard" version="1.5.0"> - <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:1.5.0</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 1274e2a62479 -r 0976a6257300 build/tools/SBMLwizard/test-data/Human-GEM_pathways.xml --- a/build/tools/SBMLwizard/test-data/Human-GEM_pathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,7661 +0,0 @@\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 1274e2a62479 -r 0976a6257300 build/tools/SBMLwizard/test-data/XF_network.sbml --- a/build/tools/SBMLwizard/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 build/tools/SBMLwizard/test-data/XF_network_C_Side.tab --- a/build/tools/SBMLwizard/test-data/XF_network_C_Side.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -M_atp_c -M_h2o_c -M_pi_c -M_adp_c -M_ppi_c -M_h_c |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SBMLwizard/test-data/XF_network_R_Seed.tab --- a/build/tools/SBMLwizard/test-data/XF_network_R_Seed.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -R_ACGS -R_GLUN |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -0,0 +1,371 @@\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="develop">\n+ <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>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CarbonSkeletonNet -i "$inputPath"\n+ -g "$inputAAM"\n+ $keepSingleCarbon\n+ $mergeComp\n+ $mergeEdges\n+ $removeIsolated\n+ $undirected\n+ $computeWeight\n+#if str($format):\n+ -f "$format"\n+#end if\n+ $main\n+ $fromIndexes\n+ -o "$output"\n+]]></command>\n+ <inputs>\n+ <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n+ <param argument="-g" format="gsam" label="input GSAM file" name="inputAAM" optional="false" type="data" value=""/>\n+ <param argument="-ks" checked="false" falsevalue="" label="keep edges involving single-carbon compounds, such as CO2 (requires formulas in SBML)" name="keepSingleCarbon" truevalue="-ks" type="boolean" value="false"/>\n+ <param argument="-mc" checked="false" falsevalue="" label="merge compartments (requires unique compound names that are consistent across compartments)" name="mergeComp" truevalue="-mc" type="boolean" value="false"/>\n+ <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>\n+ <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>\n+ <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>\n+ <param argument="-tp" checked="false" falsevalue="" label="set transition probability as weight" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>\n+ <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab">\n+ <option value="gml">gml</option>\n+ <option selected="true" value="tab">tab</option>\n+ <option value="nodeList">nodeList</option>\n+ <option value="json">json</option>\n+ <option value="matrix">matrix</option>\n+ </param>\n+ <param argument="-main" checked="false" falsevalue="" label="Compute RPAIRS-like tags and keep only main transitions for each reaction" name="main" truevalue="-main" type="boolean" value="false"/>\n+ <param argument="-fi" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-fi" type="boolean" value="false"/>\n+ </inputs>\n+ <outputs>\n+ <data format="txt" name="output"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \n+ \n+ \n+ <param name="inputPath" value="Human-GEM_pathways.xml"/>\n+ \n+ \n+ \n+ <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>\n+ \n+ \n+ \n+ <param name="format" value="gml"/>\n+ \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="2602"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ '..b' \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="2490"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \n+ \n+ \n+ <param name="inputPath" value="Human-GEM_pathways.xml"/>\n+ \n+ \n+ \n+ <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>\n+ \n+ \n+ \n+ <param name="undirected" value="true"/>\n+ \n+ \n+ \n+ <param name="format" value="gml"/>\n+ \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="3214"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \n+ \n+ \n+ <param name="inputPath" value="Human-GEM_pathways.xml"/>\n+ \n+ \n+ \n+ <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>\n+ \n+ \n+ \n+ <param name="format" value="matrix"/>\n+ \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="112"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \n+ \n+ \n+ <param name="inputPath" value="Human-GEM_pathways.xml"/>\n+ \n+ \n+ \n+ <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/>\n+ \n+ \n+ \n+ <param name="fromIndexes" value="true"/>\n+ \n+ \n+ \n+ <param name="format" value="gml"/>\n+ \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="2611"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as \'biomass\' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produces a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) performs atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help>\n+ <citations/>\n+</tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab Fri Jan 31 18:28:53 2025 +0000 |
| b |
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|
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab Fri Jan 31 18:28:53 2025 +0000 |
| b |
| b'@@ -0,0 +1,206 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. 23-21-19-17-16\tM_m01761c\t230.019153942\t23-21-19-17-16 . 9-7-5-3-2\tR_RPEc\t2.8421709430404007E-14\t23,2,3,16,5,17,7,19,9,21\n+M_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tM_m01285c\t427.02941494\t30-28-26-24-22-21-19-17-15-14\tR_HMR_4402\t79.96633052199996\t22,24,14,26,15,28,17,19,30,21\n+M_m03130c\t483.96852767\t24-22-12-11-9-6-4-3-2\tM_m03106c\t404.002197148\t24-22-12-11-9-6-4-3-2\tR_HMR_4568\t79.96633052200002\t22,11,12,24,2,3,4,6,9\n+M_m01169c\t276.024633246\t39-37-35-33-31-29\tM_m01683c\t196.058302724\t39-37-35-33-31-29\tR_HMR_4476\t79.96633052200002\t33,35,37,39,29,31\n+M_m02332l\t342.116211524\t22-20-18-16-15-12-10-8-7-5-3-2\tM_m01965l\t370.147511652\t27-22-20-18-16-15-26-12-10-8-7-5-3-2\tR_HMR_8764\t28.031300127999998\t22,12,15,16,18,2,3,5,7,8,20,10\n+M_m01690c\t169.99802457399997\t5-3-2\tM_m01842c\t260.029718626\t5-15-3-12-13-2\tR_HMR_4356\t90.031694052\t2,3,5\n+M_m02883c\t370.00661383199997\t42-40-38-36-34-28-27\tM_m02884c\t290.04028331\t42-40-38-36-34-28-27\tR_HMR_4568\t79.96633052199996\t34,36,38,27,28,40,42\n+M_m03130c\t483.96852767\t28-26-12-11-9-6-4-3-2\tM_m03107c\t566.055020568\t28-26-44-42-40-38-37-35-12-11-9-6-4-3-2\tR_HMR_8767\t82.08649289800002\t11,12,26,28,2,3,4,6,9\n+M_m01939c\t169.998024574\t9-7-5\tM_m01761c\t230.019153942\t9-7-5-3-2\tR_HMR_4501\t60.021129368000004\t5,7,9\n+M_m02845c\t230.01915394199997\t9-7-5-3-2\tM_m02846c\t230.01915394199997\t9-7-5-3-2\tR_HMR_4352\t0.0\t2,3,5,7,9\n+M_m01909c\t182.07903816799998\t53-55-57-59-51-50\tM_m01910c\t180.06338810399998\t59-57-55-53-51-50\tR_HMR_8766\t2.015650063999999\t55,57,59,50,51,53\n+M_m01322c\t260.02971862600003\t44-42-40-38-37-35\tM_m03107c\t566.055020568\t28-26-44-42-40-38-37-35-12-11-9-6-4-3-2\tR_HMR_8767\t306.025301942\t44,35,37,38,40,42\n+M_m02372c\t244.034804006\t33-41-39-37-35-36\tM_m01159c\t164.06847348399998\t41-39-37-36-35-33\tR_HMR_4402\t79.96633052200002\t33,35,36,37,39,41\n+M_m01746c\t260.029718626\t32-44-42-36-34-31\tM_m02955c\t339.99604914799994\t44-42-36-34-32-31\tR_HMR_4774\t79.96633052199996\t44,34,36,42,31,32\n+M_m01910c\t180.06338810399998\t42-40-38-36-34-33\tM_m01911c\t260.029718626\t38-40-42-33-34-36\tR_HMR_4414\t79.96633052199999\t33,34,36,38,40,42\n+M_m01371c\t506.9'..b'5.09110239\t47-45-43-37-35-33-31-30-28-26-24-23-13-12-10-9-8-7-5-4-2\tR_HMR_4306\t1.0078250319999142\t33,45,23,12,35,24,13,47,37,26,28,2,4,5,7,8,9,30,31,43,10\n+M_m01371c\t506.99574546199995\t22-20-18-17-15-13-10-11-26-24\tM_m01285c\t427.02941494\t26-24-22-20-18-17-15-13-11-10\tR_HMR_4476\t79.96633052199996\t22,11,24,13,26,15,17,18,20,10\n+M_m02555c\t745.09110239\t47-45-43-37-35-33-31-30-28-26-24-23-13-12-10-9-8-7-5-4-2\tM_m02554c\t744.083277358\t47-45-43-37-35-33-31-30-28-26-24-23-13-12-10-9-8-7-5-4-2\tR_HMR_8766\t1.0078250319999142\t33,45,23,12,35,24,13,47,37,26,28,2,4,5,7,8,9,30,31,43,10\n+M_m02034c\t522.990660082\t46-44-30-29-27-25-23-22-20-18\tM_m01951c\t605.0771529799999\t44-46-25-23-18-20-22-27-29-30-15-13-11-9-8-6\tR_HMR_4387\t82.08649289799996\t44,22,23,46,25,27,18,29,30,20\n+M_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tM_m01334c\t347.063084418\t30-28-26-24-22-21-19-17-15-14\tR_HMR_4052\t159.93266104399993\t22,24,14,26,15,28,17,19,30,21\n+M_m02884c\t290.04028331\t42-40-38-36-34-28-27\tM_m02883c\t370.00661383199997\t42-40-38-36-34-28-27\tR_HMR_4568\t79.96633052199996\t34,36,38,27,28,40,42\n+M_m02552c\t664.116946836\t43-41-39-37-35-33-31-30-28-26-24-23-13-12-10-9-7-6-5-4-2\tM_m02553c\t665.124771868\t43-41-39-37-35-33-31-30-28-26-24-23-13-12-10-9-7-6-5-4-2\tR_HMR_4315\t1.007825032000028\t33,23,12,35,24,13,37,26,39,28,2,4,5,6,7,9,41,30,31,43,10\n+M_m01951c\t605.0771529799999\t37-35-33-31-29-27-26-24-14-13-11-9-7-6-4-2\tM_m01949c\t587.066588296\t37-35-33-31-29-27-26-24-14-13-11-9-7-6-4-2\tR_HMR_4399\t18.010564683999974\t33,11,35,24,13,14,37,26,27,29,2,4,6,7,9,31\n+M_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tM_m01285c\t427.02941494\t30-28-26-24-22-21-19-17-15-14\tR_HMR_8074\t79.96633052199996\t22,24,14,26,15,28,17,19,30,21\n+M_m00812s\t340.10056146\t16-2-3-22-20-18-5-7-8-10-12-15\tM_m01965s\t370.147511652\t25-22-20-18-16-15-24-12-10-8-7-5-3-2\tR_HMR_4832\t30.046950191999997\t22,12,15,16,18,2,3,5,7,8,20,10\n+M_m02845r\t230.01915394199997\t9-7-5-3-2\tM_m02846r\t230.019153942\t9-7-5-3-2\tR_HMR_4351\t2.8421709430404007E-14\t2,3,5,7,9\n+M_m02844c\t230.019153942\t13-11-9-8-6\tM_m02845c\t230.01915394199997\t9-8-11-13-6\tR_HMR_4354\t2.8421709430404007E-14\t11,13,6,8,9\n+M_m02845c\t230.01915394199997\t23-21-19-17-16\tM_m02884c\t290.04028331\t23-21-19-17-16-3-2\tR_HMR_4501\t60.02112936800003\t23,16,17,19,21\n+M_m03107c\t566.055020568\t35-33-31-29-27-25-24-22-12-11-9-6-4-3-2\tM_m01322c\t260.02971862600003\t31-29-27-25-24-22\tR_HMR_4131\t306.025301942\t22,24,25,27,29,31\n+M_m01169c\t276.024633246\t60-58-56-54-52-50\tM_m01596c\t43.98982924\t50\tR_HMR_4474\t232.034804006\t50\n+M_m03107g\t566.055020568\t24-22-58-56-54-52-51-49-12-11-9-6-4-3-2\tM_m03106g\t404.00219714799994\t24-22-12-11-9-6-4-3-2\tR_HMR_7674\t162.0528234200001\t22,11,12,24,2,3,4,6,9\n+M_m01746c\t260.029718626\t46-44-42-41-38-37\tM_m02955c\t339.99604914799994\t44-46-37-38-42-41\tR_HMR_4775\t79.96633052199996\t44,46,37,38,41,42\n+M_m02453c\t180.06338810399998\t42-40-38-36-34-33\tM_m02455c\t260.029718626\t33-34-42-40-38-36\tR_HMR_4490\t79.96633052199999\t33,34,36,38,40,42\n+M_m01961c\t258.01406856200003\t15-13-11-5-4-2\tM_m01169c\t276.024633246\t5-4-11-13-15-2\tR_HMR_4625\t18.010564683999974\t11,13,2,4,15,5\n+M_m01745c\t180.06338810399998\t42-40-38-37-34-33\tM_tag1p_D_c\t260.029718626\t37-38-40-42-34-33\tR_KHK3\t79.96633052199999\t33,34,37,38,40,42\n+M_m01746c\t260.029718626\t15-13-11-10-7-6\tM_m01690c\t169.99802457399997\t15-7-6\tR_HMR_8762\t90.031694052\t15,6,7\n+M_m01285c\t427.02941494\t30-28-26-24-22-21-19-17-15-14\tM_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tR_HMR_9800\t79.96633052199996\t22,24,14,26,15,28,17,19,30,21\n+M_m01159c\t164.06847348399998\t41-39-37-36-35-33\tM_m02372c\t244.034804006\t33-41-39-37-35-36\tR_HMR_4402\t79.96633052200002\t33,35,36,37,39,41\n+M_m01939c\t169.998024574\t8-6-4\tM_m00640c\t214.024239322\t8-6-4-3-2\tR_HMR_4398\t44.026214748\t4,6,8\n+M_m02845c\t230.01915394199997\t40-38-36-34-33\tM_m02806c\t389.951814986\t33-40-38-36-34\tR_HMR_4052\t159.932661044\t33,34,36,38,40\n+M_m01840c\t180.06338810399998\t55-53-46-47-49-51\tM_m01682c\t182.07903816799998\t55-53-51-49-47-46\tR_HMR_4315\t2.015650063999999\t55,46,47,49,51,53\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways.xml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,163 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CompoundGraph -i "$inputPath" +#if str($inputSide) != 'None': + -sc "$inputSide" +#end if +#if str($mergingStrat): + -mc "$mergingStrat" +#end if + $mergeEdges + $removeIsolated + $degree +#if str($weightFile) != 'None': + -cw "$weightFile" +#end if + $undirected + $computeWeight +#if str($format): + -f "$format" +#end if + -o "$output" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/> + <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (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="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/> + <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> + <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/> + <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> + <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/> + <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + <test> + + + + <param name="inputPath" value="XF_network.sbml"/> + + + + <param name="inputSide" value="XF_network_C_Side.tab"/> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + + <assert_contents> + + + + <has_line_matching expression=".*node.*" n="1101"/> + + + + <has_line_matching expression=".*edge.*" n="5581"/> + + + + </assert_contents> + + + + </output> + + + + </test> + <test> + + + + <param name="inputPath" value="XF_network.sbml"/> + + + + <param name="inputSide" value="XF_network_C_Side.tab"/> + + + + <param name="undirected" value="true"/> + + + + <param name="computeWeight" value="true"/> + + + + <param name="removeIsolated" value="true"/> + + + + <param name="degree" value="true"/> + + + + <param name="mergingStrat" value="by_id"/> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + + <assert_contents> + + + + <has_line_matching expression=".*node.*" n="793"/> + + + + <has_line_matching expression=".*edge.*" n="9372"/> + + + + </assert_contents> + + + + </output> + + + + </test> + </tests> + <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. +While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations. +In contrary to the Sbml2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/Sbml2CompoundGraph/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/Sbml2CompoundGraph/test-data/XF_network.sbml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 build/tools/Sbml2CompoundGraph/test-data/XF_network_C_Side.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/Sbml2CompoundGraph/test-data/XF_network_C_Side.tab Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 build/tools/Sbml2Graph/Sbml2Graph.xml --- a/build/tools/Sbml2Graph/Sbml2Graph.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/Sbml2Graph/Sbml2Graph.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,62 +1,172 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="develop"> <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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" $bipartite $compound $reaction - $tab - $gml - -o "$outputPath" +#if str($format): + -f "$format" +#end if + -o "$output" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/> <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/> <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="export in tabulated file" name="tab" truevalue="-tab" type="boolean" value="false"/> - <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="txt" name="outputPath"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="inputPath" value="toy_model.xml"/> - <output name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + <assert_contents> - <has_n_lines n="101"/> + + + + <has_line_matching expression=".*node.*" n="8"/> + + + + <has_line_matching expression=".*edge.*" n="9"/> + + + </assert_contents> + + + </output> + + + </test> <test> + + + <param name="inputPath" value="toy_model.xml"/> + + + <param name="bipartite" value="true"/> + + + <param name="compound" value="false"/> - <output name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + <assert_contents> - <has_n_lines n="184"/> + + + + <has_line_matching expression=".*node.*" n="15"/> + + + + <has_line_matching expression=".*edge.*" n="17"/> + + + </assert_contents> + + + </output> + + + </test> <test> + + + <param name="inputPath" value="toy_model.xml"/> + + + <param name="reaction" value="true"/> + + + <param name="compound" value="false"/> - <output name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + <assert_contents> - <has_n_lines n="90"/> + + + + + <has_line_matching expression=".*node.*" n="7"/> + + + + <has_line_matching expression=".*edge.*" n="8"/> + + + + </assert_contents> + + + + </output> + + + </test> </tests> <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format. -The graph can be either a compound graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> - <citations/> +The graph can be either a compound graph, a reaction graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> + <citations> + <citation type="doi">10.1109/tcbb.2008.79</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/Sbml2PathwayNet/Sbml2PathwayNet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/Sbml2PathwayNet/Sbml2PathwayNet.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,47 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Sbml2PathwayNet" name="Sbml2PathwayNet" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2PathwayNet -i "$inputPath" +#if str($inputSide) != 'None': + -sc "$inputSide" +#end if + $removeIsolated + $onlySourcesAndSinks +#if str($weightFile) != 'None': + -cw "$weightFile" +#end if + $connectors +#if str($format): + -f "$format" +#end if + -o "$outputPath" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-sc" format="txt" label="input Side compound file (recommended)" name="inputSide" optional="true" type="data" value=""/> + <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> + <param argument="-oss" checked="false" falsevalue="" label="consider only metabolites that are source or sink in the pathway (i.e non-intermediary compounds)" name="onlySourcesAndSinks" truevalue="-oss" type="boolean" value="false"/> + <param argument="-cw" format="tsv" label="an optional file containing weights for pathway pairs" name="weightFile" optional="true" type="data" value=""/> + <param argument="-ncw" checked="false" falsevalue="" label="set number of connecting compounds as weight" name="connectors" truevalue="-ncw" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> + </inputs> + <outputs> + <data format="txt" name="outputPath"/> + </outputs> + <tests/> + <help><![CDATA[Creation of a Pathway Network representation of a SBML file content +Genome-scale metabolic networks are often partitioned into metabolic pathways. Pathways are frequently considered independently despite frequent coupling in their activity due to shared metabolites. In order to decipher the interconnections linking overlapping pathways, this app proposes the creation of "Pathway Network", where two pathways are linked if they share compounds.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/Sbml2Tab/Sbml2Tab.xml --- a/build/tools/Sbml2Tab/Sbml2Tab.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/Sbml2Tab/Sbml2Tab.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,63 +1,305 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="1.5.0"> - <description>Create a tabulated file from a SBML file</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="develop"> + <description>Create a tabulated file listing reaction 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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): - -i "$i" + -irr "$i" #end if #if str($r): - -r "$r" + -rev "$r" #end if - -in "$in" - -out "$out" + -i "$in" + -o "$out" ]]></command> <inputs> - <param argument="-i" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> + <param argument="-irr" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> </sanitizer> </param> - <param argument="-r" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>"> + <param argument="-rev" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> </sanitizer> </param> - <param argument="-in" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/> + <param argument="-i" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/> </inputs> <outputs> <data format="tsv" name="out"/> </outputs> <tests> <test> + + + + + + + + + + + <param name="in" value="toy_model.xml"/> + + + + + + + + + + + <output ftype="tsv" name="out"> - <assert_contents> - <has_n_lines n="8"/> - <has_n_columns n="9"/> - <has_text text="2.0 E[c] --> D[c]"/> - <has_text text="A[c] <==> B[c]"/> - </assert_contents> - </output> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <has_n_lines n="8"/> + + + + + + + + + + + + <has_n_columns n="9"/> + + + + + + + + + + + + <has_text text="2.0 E[c] --> D[c]"/> + + + + + + + + + + + + <has_text text="A[c] <==> B[c]"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + </test> <test> + + + + + + + + + + + <param name="in" value="toy_model.xml"/> + + + + + + + + + + + <param name="i" value="->"/> + + + + + + + + + + + <param name="r" value="="/> + + + + + + + + + + + <output ftype="tsv" name="out"> - <assert_contents> - <has_n_lines n="8"/> - <has_n_columns n="9"/> - <has_text text="2.0 E[c] -> D[c]"/> - <has_text text="A[c] = B[c]"/> - </assert_contents> - </output> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <has_n_lines n="8"/> + + + + + + + + + + + + <has_n_columns n="9"/> + + + + + + + + + + + + <has_text text="2.0 E[c] -> D[c]"/> + + + + + + + + + + + + <has_text text="A[c] = B[c]"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> - <help><![CDATA[Create a tabulated file from a SBML file]]></help> + <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> <citations/> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlCheckBalance/SbmlCheckBalance.xml --- a/build/tools/SbmlCheckBalance/SbmlCheckBalance.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/SbmlCheckBalance/SbmlCheckBalance.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,17 +1,17 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="develop"> <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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.SbmlCheckBalance -sbml "$sbml" + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.SbmlCheckBalance -i "$sbml" -out "$out" ]]></command> <inputs> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> + <param argument="-i" format="sbml" label="Input Sbml file" name="sbml" optional="false" type="data" value=""/> </inputs> <outputs> <data format="tsv" name="out"/> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml --- a/build/tools/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.5.0"> - <description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> - <xrefs> - <xref type="bio.tools">met4j</xref> - </xrefs> - <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan': - -cc "$colcharge" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p - $s -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="charges.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="chargesWithComment.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="charges.tsv"/> - <param name="nSkip" value="1"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="charges.tsv"/> - <param name="ci" value="2"/> - <param name="cc" value="3"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="chargesXF.tsv"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas -The charge must be a number. The ids must correspond between the tabulated file and the SBML file. -If prefix or suffix is different in the SBML file, use the -p or the -s options. -The charge will be written in the SBML file in two locations:+ -- in the reaction notes (e.g. <p>charge: -1</p>) -- as fbc attribute (e.g. fbc:charge="1")]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetChargesFromFile/test-data/XF_network.sbml --- a/build/tools/SbmlSetChargesFromFile/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetChargesFromFile/test-data/charges.tsv --- a/build/tools/SbmlSetChargesFromFile/test-data/charges.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A 2 -B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetChargesFromFile/test-data/chargesDifferentColumns.tsv --- a/build/tools/SbmlSetChargesFromFile/test-data/chargesDifferentColumns.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Line1 A 2 -Line2 B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetChargesFromFile/test-data/chargesWithComment.tsv --- a/build/tools/SbmlSetChargesFromFile/test-data/chargesWithComment.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#A 2 -B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetChargesFromFile/test-data/chargesXF.tsv --- a/build/tools/SbmlSetChargesFromFile/test-data/chargesXF.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -glc_D -1000 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetChargesFromFile/test-data/toy_model.xml --- a/build/tools/SbmlSetChargesFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml --- a/build/tools/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,73 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetEcsFromFile#if str($colec) != 'nan': - -cec "$colec" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cec" label="[2] number of the column where are the ecs" name="colec" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="ec.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*1.1.1.1.*" n="2"/> - <has_line_matching expression=".*1.2.3.4.*" n="2"/> - </assert_contents> - </output> - </test> - <test expect_failure="true"> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="ecBad.tsv"/> - </test> - </tests> - <help><![CDATA[Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC -The ids must correspond between the tabulated file and the SBML file. -If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. -The EC will be written in the SBML file in two locations: -- in the reaction notes (e.g. <p>EC_NUMBER: 2.4.2.14</p>) -- as a reaction annotation (e.g. <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/>)]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetEcsFromFile/test-data/ec.tsv --- a/build/tools/SbmlSetEcsFromFile/test-data/ec.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 1.1.1.1 -reac2 1.2.3.4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetEcsFromFile/test-data/ecBad.tsv --- a/build/tools/SbmlSetEcsFromFile/test-data/ecBad.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 1.1.1.1 -reac2 1.2.3.4.5 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetEcsFromFile/test-data/toy_model.xml --- a/build/tools/SbmlSetEcsFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml --- a/build/tools/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,76 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan': - -cf "$colformula" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p - $s -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cf" label="[2] number of the column where are the formulas" name="colformula" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="formula.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*CH6O6.*" n="2"/> - <has_line_matching expression=".*CH12O4.*" n="2"/> - </assert_contents> - </output> - </test> - <test expect_failure="true"> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="formulaBad.tsv"/> - </test> - </tests> - <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas -The ids must correspond between the tabulated file and the SBML file. -If prefix or suffix is different in the SBML file, use the -p or the -s options. -The formula will be written in the SBML file in two locations:+ -- in the metabolite notes (e.g. <p>formula: C16H29O2</p> - -- as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetFormulasFromFile/test-data/formula.tsv --- a/build/tools/SbmlSetFormulasFromFile/test-data/formula.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A CH6O6 -B CH12O4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetFormulasFromFile/test-data/formulaBad.tsv --- a/build/tools/SbmlSetFormulasFromFile/test-data/formulaBad.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A CH6O6 -B 12CH4O \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetFormulasFromFile/test-data/toy_model.xml --- a/build/tools/SbmlSetFormulasFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml --- a/build/tools/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,83 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan': - -cgpr "$colgpr" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cgpr" label="[2] number of the column where are the gprs" name="colgpr" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="gpr.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> - <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> - <has_line_matching expression=".*fbc:id=.G3.*" n="1"/> - <has_line_matching expression=".*fbc:id=.G4.*" n="1"/> - <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/> - <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/> - <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/> - <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/> - <has_line_matching expression=".*fbc:and.*" n="2"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[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 -The ids must correspond between the tabulated file and the SBML file. -If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. -GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307 -(The GPR will be written in the SBML file in two locations: -- in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p> -- as fbc gene product association :<fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="XC_3282"/> - <fbc:geneProductRef fbc:geneProduct="XC_0401"/> - </fbc:or> -</fbc:geneProductAssociation> -]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetGprsFromFile/test-data/gpr.tsv --- a/build/tools/SbmlSetGprsFromFile/test-data/gpr.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 G1 or G2 -reac2 G3 and G4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetGprsFromFile/test-data/gprBad.tsv --- a/build/tools/SbmlSetGprsFromFile/test-data/gprBad.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 G1 or G2 -reac2 G3 an G4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetGprsFromFile/test-data/toy_model.xml --- a/build/tools/SbmlSetGprsFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml --- a/build/tools/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,129 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetIdsFromFile" name="SbmlSetIdsFromFile" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetIdsFromFile#if str($colname) != 'nan': - -cnew "$colname" -#end if -#if str($colid): - -ci "$colid" -#end if - $p - $s -#if str($o): - -o "$o" -#end if -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="idMetabolites.tsv"/> - <param name="o" value="METABOLITE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*id=.metaboliteA.*" n="1"/> - <has_line_matching expression=".*id=.metaboliteB.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="idReactions.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*id=.reaction1.*" n="1"/> - <has_line_matching expression=".*id=.reaction2.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="idPathways.tsv"/> - <param name="o" value="PATHWAY"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*groups:id=.CEB.*" n="1"/> - <has_line_matching expression=".*groups:id=.NSP.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="idGenes.tsv"/> - <param name="o" value="GENE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> - <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="idCompartments.tsv"/> - <param name="o" value="COMPARTMENT"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*id=.cytosol.*" n="1"/> - <has_line_matching expression=".*id=.extra.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Set new ids to network objects from a tabulated file containing the old ids and the new ids -The ids must correspond between the tabulated file and the SBML file. -If prefix or suffix is different in the SBML file, use the -p or the -s options. -]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetIdsFromFile/test-data/XF_network.sbml --- a/build/tools/SbmlSetIdsFromFile/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetIdsFromFile/test-data/idCompartments.tsv --- a/build/tools/SbmlSetIdsFromFile/test-data/idCompartments.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -c cytosol -e extra \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetIdsFromFile/test-data/idGenes.tsv --- a/build/tools/SbmlSetIdsFromFile/test-data/idGenes.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -XFCFBP8418_007090 G1 -XFCFBP8418_005900 G2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetIdsFromFile/test-data/idMetabolites.tsv --- a/build/tools/SbmlSetIdsFromFile/test-data/idMetabolites.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A metaboliteA -B metaboliteB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetIdsFromFile/test-data/idPathways.tsv --- a/build/tools/SbmlSetIdsFromFile/test-data/idPathways.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Nucleotide_Salvage_Pathway NSP -Cell_Envelope_Biosynthesis CEB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetIdsFromFile/test-data/idReactions.tsv --- a/build/tools/SbmlSetIdsFromFile/test-data/idReactions.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 reaction1 -reac2 reaction2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetIdsFromFile/test-data/toy_model.xml --- a/build/tools/SbmlSetIdsFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml --- a/build/tools/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,117 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetNamesFromFile#if str($colname) != 'nan': - -cname "$colname" -#end if -#if str($colid): - -ci "$colid" -#end if - $p - $s -#if str($o): - -o "$o" -#end if -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cname" label="[2] number of the column where are the names" name="colname" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="namesMetabolites.tsv"/> - <param name="o" value="METABOLITE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*metaboliteA.*" n="1"/> - <has_line_matching expression=".*metaboliteB.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="namesReactions.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*reaction1.*" n="1"/> - <has_line_matching expression=".*reaction2.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="namesPathways.tsv"/> - <param name="o" value="PATHWAY"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*groups:name=.CEB.*" n="1"/> - <has_line_matching expression=".*groups:name=.NSP.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="namesGenes.tsv"/> - <param name="o" value="GENE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:name=.G1.*" n="1"/> - <has_line_matching expression=".*fbc:name=.G2.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Set names to network objects from a tabulated file containing the object ids and the names -The ids must correspond between the tabulated file and the SBML file. -If prefix or suffix is different in the SBML file, use the -p or the -s options. -]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetNamesFromFile/test-data/XF_network.sbml --- a/build/tools/SbmlSetNamesFromFile/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetNamesFromFile/test-data/namesGenes.tsv --- a/build/tools/SbmlSetNamesFromFile/test-data/namesGenes.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -XFCFBP8418_007090 G1 -XFCFBP8418_005900 G2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetNamesFromFile/test-data/namesMetabolites.tsv --- a/build/tools/SbmlSetNamesFromFile/test-data/namesMetabolites.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A metaboliteA -B metaboliteB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetNamesFromFile/test-data/namesPathways.tsv --- a/build/tools/SbmlSetNamesFromFile/test-data/namesPathways.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Nucleotide_Salvage_Pathway NSP -Cell_Envelope_Biosynthesis CEB |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetNamesFromFile/test-data/namesReactions.tsv --- a/build/tools/SbmlSetNamesFromFile/test-data/namesReactions.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 reaction1 -reac2 reaction2 |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetNamesFromFile/test-data/toy_model.xml --- a/build/tools/SbmlSetNamesFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml --- a/build/tools/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,97 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan': - -cp "$colp" -#end if -#if str($sep): - -sep "$sep" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cp" label="[2] number of the column where are the pathways" name="colp" optional="true" type="integer" value="2"/> - <param argument="-sep" label="[|] Separator of pathways in the tabulated file" name="sep" optional="true" type="text" value="|"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="pathways.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*groups:id=.*" n="3"/> - <has_line_matching expression=".*groups:id=.p1.*" n="1"/> - <has_line_matching expression=".*groups:id=.p2.*" n="1"/> - <has_line_matching expression=".*groups:id=.p3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="pathwaysOtherSep.tsv"/> - <param name="sep" value=" + "/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*groups:id=.*" n="3"/> - <has_line_matching expression=".*groups:id=.p1.*" n="1"/> - <has_line_matching expression=".*groups:id=.p2.*" n="1"/> - <has_line_matching expression=".*groups:id=.p3.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways -The ids must correspond between the tabulated file and the SBML file. -If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. -Pathways will be written in the SBML file in two ways:- as reaction note (e.g. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group: -<groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis"> - <groups:listOfMembers> - <groups:member groups:idRef="R_GLUPRT"/> - <groups:member groups:idRef="R_RNDR1b"/> -... -]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetPathwaysFromFile/test-data/pathways.tsv --- a/build/tools/SbmlSetPathwaysFromFile/test-data/pathways.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -reac1 P1 -reac2 P2|P3 -reac3 P1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetPathwaysFromFile/test-data/pathwaysOtherSep.tsv --- a/build/tools/SbmlSetPathwaysFromFile/test-data/pathwaysOtherSep.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -reac1 P1 -reac2 P2 + P3 -reac3 P1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetPathwaysFromFile/test-data/toy_model.xml --- a/build/tools/SbmlSetPathwaysFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml --- a/build/tools/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,88 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan': - -cr "$colRef" -#end if - -ref "$ref" -#if str($colid): - -ci "$colid" -#end if - $p - $s -#if str($o): - -o "$o" -#end if -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cr" label="[2] number of the column where are the references" name="colRef" optional="true" type="integer" value="2"/> - <param argument="-ref" label="Name of the ref. Must exist in identifiers.org" name="ref" optional="false" type="text" value=""> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="refs.tsv"/> - <param name="ref" value="InChi"/> - <param name="o" value="METABOLITE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*C2H6O.*" n="3"/> - <has_line_matching expression=".*C6H8O6.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Add refs to network objects from a tabulated file containing the metabolite ids and the formulas -Reference name given as parameter (-ref) must correspond to an existing id the registry of identifiers.org (https://registry.identifiers.org/registry) -The corresponding key:value pair will be written as metabolite or reaction annotation]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetRefsFromFile/test-data/refs.tsv --- a/build/tools/SbmlSetRefsFromFile/test-data/refs.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 -B InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-8,10-11H,1H2/t2-,5+/m0/s1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlSetRefsFromFile/test-data/toy_model.xml --- a/build/tools/SbmlSetRefsFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml --- a/build/tools/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,34 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="1.5.0"> - <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:1.5.0</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlToMetaboliteTable -s "$sbml" - -o "$outputFile" -]]></command> - <inputs> - <param argument="-s" format="sbml" label="Sbml file" name="sbml" optional="false" type="data" value=""/> - </inputs> - <outputs> - <data format="tsv" name="outputFile"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <output ftype="tsv" name="outputFile"> - <assert_contents> - <has_n_lines n="9"/> - <has_n_columns n="6"/> - <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/> - <has_line_matching expression=".*C.*NC.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlToMetaboliteTable/test-data/tests.tsv --- a/build/tools/SbmlToMetaboliteTable/test-data/tests.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,9 +0,0 @@ -id name formula charge smiles inchi -A A null 0 null null -B B null 0 null null -A_ext A_ext null 0 C[C@@H](C(=O)O)NC 1S/C2H6O/c1-2-3/h3H,2H2,1H3 -C C null 0 null null -D D null 0 null null -E E null 0 null null -D_ext D_ext null 0 null null -E_ext E_ext null 0 null null |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlToMetaboliteTable/test-data/toy_model.xml --- a/build/tools/SbmlToMetaboliteTable/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SbmlWizard/SbmlWizard.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SbmlWizard/SbmlWizard.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,231 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SbmlWizard" name="SbmlWizard" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath" +#if str($inputSide) != 'None': + -rc "$inputSide" +#end if +#if str($toKeepC) != 'None': + -kc "$toKeepC" +#end if + $removeIsolated +#if str($inputReactions) != 'None': + -rr "$inputReactions" +#end if +#if str($toKeepR) != 'None': + -kr "$toKeepR" +#end if + $removeNoFlux +#if str($mergingStrat): + -mc "$mergingStrat" +#end if + $removeDuplicated +#if str($exchangeCompToRemove): + -rEX "$exchangeCompToRemove" +#end if + -o "$outputPath" +]]></command> + <inputs> + <param argument="-i" 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="-kc" format="txt" label="file containing identifiers of compounds to keep from the metabolic network" name="toKeepC" 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="-kr" format="txt" label="file containing identifiers of reactions to keep from the metabolic network" name="toKeepR" 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 1274e2a62479 -r 0976a6257300 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 Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 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 Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 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 Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 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 Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +R_ACGS +R_GLUN |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/ScopeNetwork/ScopeNetwork.xml --- a/build/tools/ScopeNetwork/ScopeNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/ScopeNetwork/ScopeNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.5.0"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="develop"> <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:1.5.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath" -s "$seedsFilePath" @@ -17,7 +17,9 @@ -ir "$reactionToIgnoreFile" #end if $trace - $asTable +#if str($format): + -f "$format" +#end if -o "$output" ]]></command> <inputs> @@ -27,26 +29,67 @@ <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/> <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope" name="reactionToIgnoreFile" optional="true" type="data" value=""/> <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="output"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="sbmlFilePath" value="toy_model.xml"/> + + + <param name="seedsFilePath" value="seeds.txt"/> + + + <param name="sideCompoundFile" value="sides.txt"/> - <output ftype="gml" name="output"> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + <assert_contents> + + + <has_line_matching expression=".*node.*" n="9"/> + + + <has_line_matching expression=".*edge.*" n="11"/> + + + </assert_contents> + + + </output> + + + </test> </tests> <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network -The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction -For more information, see Handorf, Ebenhöh and Heinrich (2005). *Expanding metabolic networks: scopes of compounds, robustness, and evolution.* Journal of molecular evolution, 61(4), 498-512. (https://doi.org/10.1007/s00239-005-0027-1)]]></help> - <citations/> +The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction]]></help> + <citations> + <citation type="doi">10.1007/s00239-005-0027-1</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SeedsAndTargets/SeedsAndTargets.xml --- a/build/tools/SeedsAndTargets/SeedsAndTargets.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/SeedsAndTargets/SeedsAndTargets.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="1.5.0">\n- <description>Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology</description>\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="develop">\n+ <description>Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath"\n #if str($inputSide) != \'None\':\n@@ -25,18 +25,18 @@\n ]]></command>\n <inputs>\n <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n- <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>\n- <param argument="-c" label="Selected compartment(s), as model identifiers, separated by "+" sign if more than one" name="comp" optional="true" type="text" value="">\n+ <param argument="-sc" format="txt" label="input side compound file" name="inputSide" optional="true" type="data" value=""/>\n+ <param argument="-c" label="selected compartment(s), as model identifiers, separated by "+" sign if more than one" name="comp" optional="true" type="text" value="">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n <param argument="-s" checked="false" falsevalue="" label="export seeds" name="source" truevalue="-s" type="boolean" value="false"/>\n <param argument="-t" checked="false" falsevalue="" label="export targets" name="sink" truevalue="-t" type="boolean" value="false"/>\n- <param argument="-!s" checked="false" falsevalue="" label="export nodes that are not seed" name="notsource" truevalue="-!s" type="boolean" value="false"/>\n+ <param argument="-!s" checked="false" falsevalue="" label="export nodes that are not seeds" name="notsource" truevalue="-!s" type="boolean" value="false"/>\n <param argument="-!t" checked="false" falsevalue="" label="export nodes that are not targets" name="notsink" truevalue="-!t" type="boolean" value="false"/>\n- <param argument="-is" checked="false" falsevalue="" label="do not ignore isolated nodes, consider isolated both seed and target" name="keepIsolated" truevalue="-is" type="boolean" value="false"/>\n- <param argument="-B" checked="false" falsevalue="" label="use Borenstein Algorithm. Please cite Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105). ignore internal option" name="useBorensteinAlg" truevalue="-B" type="boolean" value="false"/>\n+ <param argument="-is" checked="false" falsevalue="" label="do not ignore isolated nodes, consider isolated both seeds and targets" name="keepIsolated" truevalue="-is" type="boolean" value="false"/>\n+ <param argument="-B" checked="false" falsevalue="" label="use Borenstein Algorithm. Please cite Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105), ignore internal option" name="useBorensteinAlg" truevalue="-B" type="boolean" value="false"/>\n <param argument="-in" checked="false" falsevalue="" label="if an external compartment is defined, adjust degree by considering internal counterpart"'..b'Path">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_columns n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="26"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="^M_\\S+_\\w" n="26"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n- <help><![CDATA[Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology. Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms.\n+ <help><![CDATA[Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology\n+Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms.\n This application can use seed definition and SCC-based detection algorithm by Borenstein et al. or, alternatively, degree-based sink and source detection with compartment adjustment.\n-The first method (see Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105) consider strongly connected components rather than individual nodes, thus, members of cycles can be considered as seed. A sink from an external compartment can however be connected to a non sink internal counterpart, thus highlighting what could end up in the external compartment rather than what must be exported.\n+The first method (see Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105) consider strongly connected components rather than individual nodes, thus, members of cycles can be considered as seeds. A sink from an external compartment can however be connected to a non sink internal counterpart, thus highlighting what could end up in the external compartment rather than what must be exported.\n The second approach is neighborhood based and identify sources and sinks. Since "real" sinks and sources in intracellular compartment(s) may be involved in transport/exchange reactions reversible by default, thus not allowing extracellular source or sink, an option allows to take the degree (minus extracellular neighbors) of intracellular counterparts.]]></help>\n- <citations/>\n+ <citations>\n+ <citation type="doi">10.1073/pnas.0806162105</citation>\n+ </citations>\n </tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetCharges/SetCharges.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetCharges/SetCharges.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -0,0 +1,445 @@\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SetCharges" name="SetCharges" version="develop">\n+ <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</description>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetCharges#if str($colcharge) != \'nan\':\n+ -cc "$colcharge"\n+#end if\n+#if str($colid) != \'nan\':\n+ -ci "$colid"\n+#end if\n+ $p\n+ $s\n+#if str($nSkip):\n+ -n "$nSkip"\n+#end if\n+ -i "$sbml"\n+#if str($tab) != \'None\':\n+ -tab "$tab"\n+#end if\n+#if str($c):\n+ -c "$c"\n+#end if\n+ -o "$out"\n+]]></command>\n+ <inputs>\n+ <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" optional="true" type="integer" value="2"/>\n+ <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/>\n+ <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/>\n+ <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>\n+ <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>\n+ <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>\n+ <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won\'t be read" name="c" optional="true" type="text" value="#">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data format="sbml" name="out"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="toy_model.xml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="charges.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param na'..b' \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="toy_model.xml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="charges.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="ci" value="2"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="cc" value="3"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="chargesXF.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="p" value="true"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="s" value="true"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges\n+The charge must be a number. The ids must correspond between the tabulated file and the SBML file.\n+If prefix or suffix is different in the SBML file, use the -p or the -s options.\n+The charge will be written in the SBML file in two locations:+\n+- in the reaction notes (e.g. charge: -1)\n+- as fbc attribute (e.g. fbc:charge="1")]]></help>\n+ <citations>\n+ <citation type="doi">10.1515/jib-2017-0082</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetCharges/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetCharges/test-data/XF_network.sbml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 build/tools/SetCharges/test-data/charges.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetCharges/test-data/charges.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A 2 +B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetCharges/test-data/chargesDifferentColumns.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetCharges/test-data/chargesDifferentColumns.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Line1 A 2 +Line2 B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetCharges/test-data/chargesWithComment.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetCharges/test-data/chargesWithComment.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#A 2 +B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetCharges/test-data/chargesXF.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetCharges/test-data/chargesXF.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,1 @@ +glc_D -1000 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetCharges/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetCharges/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetChemicalFormulas/SetChemicalFormulas.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetChemicalFormulas/SetChemicalFormulas.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,155 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetChemicalFormulas#if str($colformula) != 'nan': + -cf "$colformula" +#end if +#if str($colid) != 'nan': + -ci "$colid" +#end if + $p + $s +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cf" label="[2] number of the column where are the formulas" name="colformula" optional="true" type="integer" value="2"/> + <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="formula.tsv"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*CH6O6.*" n="2"/> + + + + + + + <has_line_matching expression=".*CH12O4.*" n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test expect_failure="true"> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="formulaBad.tsv"/> + + + + + + + </test> + </tests> + <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas +The ids must correspond between the tabulated file and the SBML file. +If prefix or suffix is different in the SBML file, use the -p or the -s options. +The formula will be written in the SBML file in two locations:+ +- in the metabolite HTML notes (e.g. formula: C16H29O2) +- as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")]]></help> + <citations> + <citation type="doi">10.1515/jib-2017-0082</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetChemicalFormulas/test-data/formula.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetChemicalFormulas/test-data/formula.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A CH6O6 +B CH12O4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetChemicalFormulas/test-data/formulaBad.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetChemicalFormulas/test-data/formulaBad.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A CH6O6 +B 12CH4O \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetChemicalFormulas/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetChemicalFormulas/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetEcNumbers/SetEcNumbers.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetEcNumbers/SetEcNumbers.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,153 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetEcNumbers" name="SetEcNumbers" version="develop"> + <description>Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetEcNumbers#if str($colec) != 'nan': + -cec "$colec" +#end if +#if str($colid) != 'nan': + -ci "$colid" +#end if + $p +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cec" label="[2] number of the column where are the ecs" name="colec" optional="true" type="integer" value="2"/> + <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="ec.tsv"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*1.1.1.1.*" n="2"/> + + + + + + + <has_line_matching expression=".*1.2.3.4.*" n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test expect_failure="true"> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="ecBad.tsv"/> + + + + + + + </test> + </tests> + <help><![CDATA[Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers +The ids must correspond between the tabulated file and the SBML file. +If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. +The EC will be written in the SBML file in two locations: +- in the reaction HTML notes (e.g. EC_NUMBER: 2.4.2.14) +- as a reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/) with ec-code identifiers link (https://registry.identifiers.org/registry/ec-code)]]></help> + <citations> + <citation type="doi">10.1038/nbt1156</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetEcNumbers/test-data/ec.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetEcNumbers/test-data/ec.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 1.1.1.1 +reac2 1.2.3.4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetEcNumbers/test-data/ecBad.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetEcNumbers/test-data/ecBad.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 1.1.1.1 +reac2 1.2.3.4.5 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetEcNumbers/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetEcNumbers/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetGprs/SetGprs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetGprs/SetGprs.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,182 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetGprs" name="SetGprs" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetGprs#if str($colgpr) != 'nan': + -cgpr "$colgpr" +#end if +#if str($colid) != 'nan': + -ci "$colid" +#end if + $p +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cgpr" label="[2] number of the column where are the gprs" name="colgpr" optional="true" type="integer" value="2"/> + <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="gpr.tsv"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:id=.G3.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:id=.G4.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:and.*" n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[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 +The ids must correspond between the tabulated file and the SBML file. +If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. +GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307 +(The GPR will be written in the SBML file in two locations: +- in the reaction html notes (GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )) +- as fbc gene product association (see FBC package specifications: https://doi.org/10.1515/jib-2017-0082)]]></help> + <citations> + <citation type="doi">10.1038/nprot.2011.308</citation> + <citation type="doi">10.1515/jib-2017-0082</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetGprs/test-data/gpr.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetGprs/test-data/gpr.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 G1 or G2 +reac2 G3 and G4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetGprs/test-data/gprBad.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetGprs/test-data/gprBad.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 G1 or G2 +reac2 G3 an G4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetGprs/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetGprs/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetIds/SetIds.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetIds/SetIds.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -0,0 +1,453 @@\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SetIds" name="SetIds" version="develop">\n+ <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</description>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetIds#if str($colname) != \'nan\':\n+ -cnew "$colname"\n+#end if\n+#if str($colid):\n+ -ci "$colid"\n+#end if\n+ $p\n+ $s\n+#if str($o):\n+ -t "$o"\n+#end if\n+#if str($nSkip):\n+ -n "$nSkip"\n+#end if\n+ -i "$sbml"\n+#if str($tab) != \'None\':\n+ -tab "$tab"\n+#end if\n+#if str($c):\n+ -c "$c"\n+#end if\n+ -o "$out"\n+]]></command>\n+ <inputs>\n+ <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/>\n+ <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>\n+ <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>\n+ <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>\n+ <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>\n+ <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won\'t be read" name="c" optional="true" type="text" value="#">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data format="sbml" name="out"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="toy_model.xml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="idMetabolites.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="METABOLITE"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ '..b'+ \n+ <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="idGenes.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="GENE"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="idCompartments.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="COMPARTMENT"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*id=.cytosol.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*id=.extra.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids\n+The ids must correspond between the tabulated file and the SBML file.\n+If prefix or suffix is different in the SBML file, use the -p or the -s options.\n+]]></help>\n+ <citations/>\n+</tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetIds/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetIds/test-data/XF_network.sbml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 build/tools/SetIds/test-data/idCompartments.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetIds/test-data/idCompartments.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +c cytosol +e extra \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetIds/test-data/idGenes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetIds/test-data/idGenes.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +XFCFBP8418_007090 G1 +XFCFBP8418_005900 G2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetIds/test-data/idMetabolites.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetIds/test-data/idMetabolites.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A metaboliteA +B metaboliteB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetIds/test-data/idPathways.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetIds/test-data/idPathways.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Nucleotide_Salvage_Pathway NSP +Cell_Envelope_Biosynthesis CEB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetIds/test-data/idReactions.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetIds/test-data/idReactions.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 reaction1 +reac2 reaction2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetIds/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetIds/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetNames/SetNames.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetNames/SetNames.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -0,0 +1,375 @@\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SetNames" name="SetNames" version="develop">\n+ <description>Set names to network objects in a SBML file from a tabulated file containing the object ids and the names</description>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetNames#if str($colname) != \'nan\':\n+ -cname "$colname"\n+#end if\n+#if str($colid):\n+ -ci "$colid"\n+#end if\n+ $p\n+ $s\n+#if str($o):\n+ -t "$o"\n+#end if\n+#if str($nSkip):\n+ -n "$nSkip"\n+#end if\n+ -i "$sbml"\n+#if str($tab) != \'None\':\n+ -tab "$tab"\n+#end if\n+#if str($c):\n+ -c "$c"\n+#end if\n+ -o "$out"\n+]]></command>\n+ <inputs>\n+ <param argument="-cname" label="[2] number of the column where are the names" name="colname" optional="true" type="integer" value="2"/>\n+ <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>\n+ <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>\n+ <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>\n+ <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>\n+ <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won\'t be read" name="c" optional="true" type="text" value="#">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data format="sbml" name="out"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="toy_model.xml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="namesMetabolites.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="METABOLITE"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*metaboliteA.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ '..b' \n+ <has_line_matching expression=".*reaction1.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*reaction2.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="namesPathways.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="PATHWAY"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*groups:name=.CEB.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*groups:name=.NSP.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="namesGenes.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="GENE"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:name=.G1.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:name=.G2.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Set names to network objects in a SBML file from a tabulated file containing the object ids and the names\n+The ids must correspond between the tabulated file and the SBML file.\n+If prefix or suffix is different in the SBML file, use the -p or the -s options.\n+]]></help>\n+ <citations/>\n+</tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetNames/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetNames/test-data/XF_network.sbml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 build/tools/SetNames/test-data/namesGenes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetNames/test-data/namesGenes.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +XFCFBP8418_007090 G1 +XFCFBP8418_005900 G2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetNames/test-data/namesMetabolites.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetNames/test-data/namesMetabolites.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A metaboliteA +B metaboliteB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetNames/test-data/namesPathways.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetNames/test-data/namesPathways.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Nucleotide_Salvage_Pathway NSP +Cell_Envelope_Biosynthesis CEB |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetNames/test-data/namesReactions.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetNames/test-data/namesReactions.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 reaction1 +reac2 reaction2 |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetNames/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetNames/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetPathways/SetPathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetPathways/SetPathways.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,243 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetPathways" name="SetPathways" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetPathways#if str($colp) != 'nan': + -cp "$colp" +#end if +#if str($sep): + -sep "$sep" +#end if +#if str($colid) != 'nan': + -ci "$colid" +#end if + $p +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cp" label="[2] number of the column where are the pathways" name="colp" optional="true" type="integer" value="2"/> + <param argument="-sep" label="[|] Separator of pathways in the tabulated file" name="sep" optional="true" type="text" value="|"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="pathways.tsv"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*groups:id=.*" n="3"/> + + + + + + + <has_line_matching expression=".*groups:id=.p1.*" n="1"/> + + + + + + + <has_line_matching expression=".*groups:id=.p2.*" n="1"/> + + + + + + + <has_line_matching expression=".*groups:id=.p3.*" n="1"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="pathwaysOtherSep.tsv"/> + + + + + + + <param name="sep" value=" + "/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*groups:id=.*" n="3"/> + + + + + + + <has_line_matching expression=".*groups:id=.p1.*" n="1"/> + + + + + + + <has_line_matching expression=".*groups:id=.p2.*" n="1"/> + + + + + + + <has_line_matching expression=".*groups:id=.p3.*" n="1"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways +The ids must correspond between the tabulated file and the SBML file. +If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. +Pathways will be written in the SBML file in two ways:- as reaction note (e.g. SUBSYSTEM: purine_biosynthesis)- as SBML group (see Group package specifications: https://pmc.ncbi.nlm.nih.gov/articles/PMC5451322/)]]></help> + <citations> + <citation type="doi">10.1515/jib-2016-290</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetPathways/test-data/pathways.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetPathways/test-data/pathways.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,3 @@ +reac1 P1 +reac2 P2|P3 +reac3 P1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetPathways/test-data/pathwaysOtherSep.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetPathways/test-data/pathwaysOtherSep.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,3 @@ +reac1 P1 +reac2 P2 + P3 +reac3 P1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetPathways/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetPathways/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetReferences/SetReferences.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetReferences/SetReferences.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,162 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetReferences" name="SetReferences" version="develop"> + <description>Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetReferences#if str($colRef) != 'nan': + -cr "$colRef" +#end if + -ref "$ref" +#if str($colid): + -ci "$colid" +#end if + $p + $s +#if str($o): + -t "$o" +#end if +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cr" label="[2] number of the column where are the references" name="colRef" optional="true" type="integer" value="2"/> + <param argument="-ref" label="Name of the reference. Must exist in identifiers.org (https://registry.identifiers.org/registry)" name="ref" optional="false" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> + <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="refs.tsv"/> + + + + + + + <param name="ref" value="InChi"/> + + + + + + + <param name="o" value="METABOLITE"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*C2H6O.*" n="3"/> + + + + + + + <has_line_matching expression=".*C6H8O6.*" n="1"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references +Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry) +The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)]]></help> + <citations> + <citation type="doi">10.1038/nbt1156</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetReferences/test-data/refs.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetReferences/test-data/refs.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 +B InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-8,10-11H,1H2/t2-,5+/m0/s1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SetReferences/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SetReferences/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/SideCompoundsScan/SideCompoundsScan.xml --- a/build/tools/SideCompoundsScan/SideCompoundsScan.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/SideCompoundsScan/SideCompoundsScan.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="1.5.0">\n- <description>Scan a network to identify side-compounds.</description>\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="develop">\n+ <description>Scan a network to identify side compounds.</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath"\n $sideOnly\n@@ -28,18 +28,18 @@\n ]]></command>\n <inputs>\n <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n- <param argument="-s" checked="false" falsevalue="" label="output compounds flagged as side-Compounds only" name="sideOnly" truevalue="-s" type="boolean" value="false"/>\n- <param argument="-id" checked="false" falsevalue="" label="do not report values in output, export ids list of compounds flagged as side-Compounds, allowing piping results" name="noReportValue" truevalue="-id" type="boolean" value="false"/>\n- <param argument="-d" label="flag as side compounds any compounds with degree above threshold" name="degree" optional="true" type="text" value="400">\n+ <param argument="-s" checked="false" falsevalue="" label="output compounds flagged as side compounds only" name="sideOnly" truevalue="-s" type="boolean" value="false"/>\n+ <param argument="-id" checked="false" falsevalue="" label="do not report values in output, export ids of compounds flagged as side compounds, allowing piping results" name="noReportValue" truevalue="-id" type="boolean" value="false"/>\n+ <param argument="-d" label="flag as side compounds any compound with degree above threshold" name="degree" optional="true" type="text" value="400">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n <param argument="-dp" label="flag as side compounds the top x% of compounds according to their degree" name="degreePrecentile" optional="true" type="float" value="NaN"/>\n- <param argument="-cc" checked="false" falsevalue="" label="flag as side compound any compounds with less than 2 carbons in formula" name="flagInorganic" truevalue="-cc" type="boolean" value="false"/>\n- <param argument="-uf" checked="false" falsevalue="" label="flag as side compound any compounds with no valid chemical formula" name="flagNoFormula" truevalue="-uf" type="boolean" value="false"/>\n+ <param argument="-cc" checked="false" falsevalue="" label="flag as side compound any compound with less than 2 carbons in formula" name="flagInorganic" truevalue="-cc" type="boolean" value="false"/>\n+ <param argument="-uf" checked="false" falsevalue="" label="flag as side compound any compound with no valid chemical formula" name="flagNoFormula" truevalue="-uf" type="boolean" value="false"/>\n <param argument="-nc" label="flag as side compound any compound with a number of parallel edges shared with a neighbor above the given threshold" name="parallelEdge" optional="true" type="float" value="NaN"/>\n- <param argument="-m" label="Degree is shared between compounds in different compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">\n+ <param argument="-m" label="degree is shared between compounds in different compartments. Use names if consistent and unambiguo'..b'"tsv" name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="6"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_columns n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n- <help><![CDATA[Scan a network to identify side-compounds.\n+ <help><![CDATA[Scan a network to identify side compounds.\n Side compounds are metabolites of small relevance for topological analysis. Their definition can be quite subjective and varies between sources.\n Side compounds tend to be ubiquitous and not specific to a particular biochemical or physiological process.Compounds usually considered as side compounds include water, atp or carbon dioxide. By being involved in many reactions and thus connected to many compounds, they tend to significantly lower the average shortest path distances beyond expected metabolic relatedness.\n This tool attempts to propose a list of side compounds according to specific criteria: \n - *Degree*: Compounds with an uncommonly high number of neighbors can betray a lack of process specificity. \n High degree compounds typically include water and most main cofactors (CoA, ATP, NADPH...) but can also include central compounds such as pyruvate or acetyl-CoA \n - *Neighbor Coupling*: Similar to degree, this criteria assume that side compounds are involved in many reactions, but in pairs with other side compounds.\n-Therefore, the transition from ATP to ADP will appear multiple time in the network, creating redundant \'parallel edges\' between these two neighbors.\n+Therefore, the transition from ATP to ADP will appear multiple times in the network, creating redundant \'parallel edges\' between these two neighbors.\n Being tightly coupled to another compound through a high number of redundant edges, can point out cofactors while keeping converging pathways\' products with high degree like pyruvate aside. \n - *Carbon Count*: Metabolic "waste", or degradation end-product such as ammonia or carbon dioxide are usually considered as side compounds.\n Most of them are inorganic compound, another ill-defined concept, sometimes defined as compound lacking C-C or C-H bonds. Since chemical structure is rarely available in SBML model beyond chemical formula, we use a less restrictive criterion by flagging compound with one or no carbons. This cover most inorganic compounds, but include few compounds such as methane usually considered as organic. - *Chemical Formula*: Metabolic network often contains \'artifacts\' that serve modelling purpose (to define a composite objective function for example). Such entities can be considered as \'side entities\'. Since they are not actual chemical compounds, they can be detected by their lack of valid chemical formula. However, this can also flag main compounds with erroneous or missing annotation.]]></help>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/Tab2Sbml/Tab2Sbml.xml --- a/build/tools/Tab2Sbml/Tab2Sbml.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/Tab2Sbml/Tab2Sbml.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.5.0">\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="develop">\n <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != \'nan\':\n -ci "$colid"\n@@ -19,12 +19,12 @@\n -e "$e"\n #end if\n #if str($i):\n- -i "$i"\n+ -irr "$i"\n #end if\n #if str($r):\n- -r "$r"\n+ -rev "$r"\n #end if\n- -in "$in"\n+ -i "$in"\n #if str($id):\n -id "$id"\n #end if\n@@ -35,7 +35,7 @@\n #if str($nSkip) != \'nan\':\n -n "$nSkip"\n #end if\n- -sbml "$sbml"\n+ -o "$sbml"\n ]]></command>\n <inputs>\n <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/>\n@@ -47,17 +47,17 @@\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n- <param argument="-i" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->">\n+ <param argument="-irr" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n- <param argument="-r" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>">\n+ <param argument="-rev" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n- <param argument="-in" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/>\n+ <param argument="-i" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/>\n <param argument="-id" label="[NA] Model id written in the SBML file" name="id" optional="true" type="text" value="NA">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n@@ -76,63 +76,657 @@\n </outputs>\n <tests>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="in" value="toy_model.tsv"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="sbml" name="sbml">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <is_valid_xml/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*reaction .*" n="7"/>\n+ \n+ \n+ \n+ \n+ \n+ '..b' \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <is_valid_xml/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*id=.R_reac2.*" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="in" value="toy_model.tsv"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="id" value="myModel"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="sbml" name="sbml">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <is_valid_xml/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*myModel.*" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml --- a/build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,13 +1,13 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_TopologicalPathwayAnalysis" name="TopologicalPathwayAnalysis" version="1.5.0">\n- <description>Run a Topological Pathway Analysis to identify key pathways based on topological properties of its constituting compounds.</description>\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_TopologicalPathwayAnalysis" name="TopologicalPathwayAnalysis" version="develop">\n+ <description>Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds.</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n- <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.TopologicalPathwayAnalysis -s "$inputPath"\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.TopologicalPathwayAnalysis -i "$inputPath"\n #if str($inputSide) != \'None\':\n -sc "$inputSide"\n #end if\n@@ -24,7 +24,7 @@\n -o "$outputPath"\n ]]></command>\n <inputs>\n- <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n+ <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n <param argument="-sc" format="txt" label="input Side compound file (recommended)" name="inputSide" optional="true" type="data" value=""/>\n <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">\n <option selected="true" value="no">no</option>\n@@ -42,32 +42,297 @@\n </outputs>\n <tests>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputPath" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="dataPath" value="XF_network_C_NOI.txt"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputSide" value="XF_network_C_Side.tab"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_columns n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_co'..b' \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="removeIsolated" value="true"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="out" value="true"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="mergingStrat" value="by_id"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_columns n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n- <help><![CDATA[Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its mapped compounds. From a list of compounds of interest, the app compute their betweenness centrality (which quantifies how often a compound acts as a intermediary along the shortest paths between pairs of other compounds in the network, which, if high, suggest a critical role in the overall flow within the network). Each pathway is scored according to the summed centrality of its metabolites found in the dataset. Alternatively to the betweenness, one can make use of the out-degree (the number of outgoing link, i.e. number of direct metabolic product) as a criterion of importance. TPA is complementary to statistical enrichment analysis to ensures a more meaningful interpretation of the data, by taking into account the influence of identified compounds on the structure of the pathways.]]></help>\n+ <help><![CDATA[Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds.\n+From a list of compounds of interest, the app compute their betweenness centrality (which quantifies how often a compound acts as a intermediary along the shortest paths between pairs of other compounds in the network, which, if high, suggest a critical role in the overall flow within the network). Each pathway is scored according to the summed centrality of its metabolites found in the dataset. Alternatively to the betweenness, one can make use of the out-degree (the number of outgoing link, i.e. number of direct metabolic product) as a criterion of importance. TPA is complementary to statistical enrichment analysis to ensures a more meaningful interpretation of the data, by taking into account the influence of identified compounds on the structure of the pathways.]]></help>\n <citations/>\n </tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 met4j-galaxy.iml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/met4j-galaxy.iml Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="true"> + <exclude-output /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/planemo/lib/python3.8/site-packages/schema_salad/java/main_utils" isTestSource="false" packagePrefix="$" /> + <sourceFolder url="file://$MODULE_DIR$/planemo/lib/python3.8/site-packages/schema_salad/java/test_utils" isTestSource="false" packagePrefix="$" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + </component> +</module> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tests.html --- a/tests.html Wed Jul 26 15:33:45 2023 +0000 +++ b/tests.html Fri Jan 31 18:28:53 2025 +0000 |
| b |
| b"@@ -285,7 +285,7 @@\n var md = window.markdownit({\n html: true,\n });\n- target.innerHTML = md.render(atob('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"..b"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</script>\n </body>\n </html>\n\\ No newline at end of file\n" |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/DecomposeSBML/DecomposeSBML.xml --- a/tools/attributes/DecomposeSBML/DecomposeSBML.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,60 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_DecomposeSBML" name="DecomposeSBML" version="MET4J_VERSION_TEST"> - <description>Parse SBML to render list of composing entities: metabolites, reactions, genes and others.</description> - <xrefs> - <xref type="bio.tools">met4j</xref> - </xrefs> - <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.DecomposeSBML -i "$sbml" - $printMetabolites - $printReactions - $printCompartments - $printPathways - $printGenes - $noTypeCol - -o "$outputFile" -]]></command> - <inputs> - <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/> - <param argument="-m" checked="false" falsevalue="" label="Extract Metabolites" name="printMetabolites" truevalue="-m" type="boolean" value="false"/> - <param argument="-r" checked="false" falsevalue="" label="Extract Reactions" name="printReactions" truevalue="-r" type="boolean" value="false"/> - <param argument="-c" checked="false" falsevalue="" label="Extract Compartments" name="printCompartments" truevalue="-c" type="boolean" value="false"/> - <param argument="-p" checked="false" falsevalue="" label="Extract Pathways" name="printPathways" truevalue="-p" type="boolean" value="false"/> - <param argument="-g" checked="false" falsevalue="" label="Extract Genes" name="printGenes" truevalue="-g" type="boolean" value="false"/> - <param argument="-nt" checked="false" falsevalue="" label="Do not output type column" name="noTypeCol" truevalue="-nt" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="tsv" name="outputFile"/> - </outputs> - <tests> - <test> - <param name="sbml" value="Human-GEM_pathways.xml"/> - <output ftype="tsv" name="outputFile"> - <assert_contents> - <has_text_matching expression="GENE" n="86"/> - <has_text_matching expression="METABOLITE" n="111"/> - <has_text_matching expression="REACTION" n="75"/> - <has_text_matching expression="PATHWAY" n="3"/> - <has_text_matching expression="COMPARTMENT" n="5"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="Human-GEM_pathways.xml"/> - <param name="printReactions" value="true"/> - <param name="printMetabolites" value="true"/> - <param name="printGenes" value="true"/> - <param name="printCompartments" value="true"/> - <param name="noTypeCol" value="true"/> - <output ftype="tsv" name="outputFile"> - <assert_contents> - <has_n_lines n="277"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Parse SBML to render list of composing entities: metabolites, reactions, genes, pathways and compartments. The output file is a tsv with two columns, one with entities identifiers, and one with the entity type. If no entity type is selected, by default all of them are taken into account. Only identifiers are written, attributes can be extracted from dedicated apps or from the SBML2Tab.]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/DecomposeSBML/test-data/Human-GEM_pathways.xml --- a/tools/attributes/DecomposeSBML/test-data/Human-GEM_pathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,7661 +0,0 @@\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 1274e2a62479 -r 0976a6257300 tools/attributes/ExtractAnnotations/ExtractAnnotations.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/ExtractAnnotations/ExtractAnnotations.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,273 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="develop"> + <description>Extract databases' references from SBML annotations or notes.</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractAnnotations -i "$inputPath" + -export "$export" + -db "$db" + $uniq + $skip + -o "$outputPath" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-export" label="the type of entity to extract annotation, either metabolite, reaction, or gene" name="export" optional="false" type="select" value="METABOLITE"> + <option selected="true" value="METABOLITE">METABOLITE</option> + <option value="REACTION">REACTION</option> + <option value="GENE">GENE</option> + </param> + <param argument="-db" label="name of the referenced database to export annotations from, as listed in notes or identifiers.org base uri" name="db" optional="false" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-uniq" checked="false" falsevalue="" label="keep only one identifier if multiple are referenced for the same entity" name="uniq" truevalue="-uniq" type="boolean" value="false"/> + <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/> + </inputs> + <outputs> + <data format="tsv" name="outputPath"/> + </outputs> + <tests> + <test> + + + + + + + <param name="inputPath" value="Human-GEM_pathways.xml"/> + + + + + + + <param name="export" value="METABOLITE"/> + + + + + + + <param name="db" value="metanetx.chemical"/> + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="146"/> + + + + + + + <has_n_columns n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test> + + + + + + + <param name="inputPath" value="Human-GEM_pathways.xml"/> + + + + + + + <param name="export" value="METABOLITE"/> + + + + + + + <param name="db" value="metanetx.chemical"/> + + + + + + + <param name="skip" value="true"/> + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="145"/> + + + + + + + <has_n_columns n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test> + + + + + + + <param name="inputPath" value="Human-GEM_pathways.xml"/> + + + + + + + <param name="export" value="METABOLITE"/> + + + + + + + <param name="db" value="metanetx.chemical"/> + + + + + + + <param name="skip" value="true"/> + + + + + + + <param name="uniq" value="true"/> + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="111"/> + + + + + + + <has_n_columns n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/ExtractAnnotations/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/ExtractAnnotations/test-data/Human-GEM_pathways.xml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 tools/attributes/ExtractPathways/ExtractPathways.xml --- a/tools/attributes/ExtractPathways/ExtractPathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/attributes/ExtractPathways/ExtractPathways.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractPathways" name="ExtractPathways" version="MET4J_VERSION_TEST"> - <description>Extract pathway(s) from GSMN</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractPathways" name="ExtractPathways" version="develop"> + <description>Extract pathway(s) from a SBML file and create a sub-network SBML file</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> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath" -p "$pathwayId" @@ -24,17 +24,127 @@ </outputs> <tests> <test> + + + + + + + + + + + <param name="inputPath" value="XF_network.sbml"/> + + + + + + + + + + + <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/> + + + + + + + + + + + <output ftype="sbml" name="outputPath"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*<reaction.*" n="17"/> - <has_line_matching expression=".*groups:id=.*" n="2"/> - </assert_contents> - </output> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <is_valid_xml/> + + + + + + + + + + + + <has_line_matching expression=".*<reaction.*" n="17"/> + + + + + + + + + + + + <has_line_matching expression=".*groups:id=.*" n="2"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> - <help><![CDATA["Extract pathway(s) from GSMN: From a SBML file, Create a sub-network SBML file including only a selection of pathways]]></help> + <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file]]></help> <citations/> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml --- a/tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,75 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="MET4J_VERSION_TEST"> - <description>Extract databases' references from SBML annotations or notes.</description> - <xrefs> - <xref type="bio.tools">met4j</xref> - </xrefs> - <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractSbmlAnnot -i "$inputPath" - -export "$export" - -db "$db" - $uniq - $skip - -o "$outputPath" -]]></command> - <inputs> - <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-export" label="the type of entity to extract annotation, either metabolite, reaction, or gene" name="export" optional="false" type="select" value="METABOLITE"> - <option selected="true" value="METABOLITE">METABOLITE</option> - <option value="REACTION">REACTION</option> - <option value="GENE">GENE</option> - </param> - <param argument="-db" label="name of the referenced database to export annotations from, as listed in notes or identifiers.org base uri" name="db" optional="false" type="text" value=""> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-uniq" checked="false" falsevalue="" label="keep only one identifier if multiple are referenced for the same entity" name="uniq" truevalue="-uniq" type="boolean" value="false"/> - <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="tsv" name="outputPath"/> - </outputs> - <tests> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="export" value="METABOLITE"/> - <param name="db" value="metanetx.chemical"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="146"/> - <has_n_columns n="2"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="export" value="METABOLITE"/> - <param name="db" value="metanetx.chemical"/> - <param name="skip" value="true"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="145"/> - <has_n_columns n="2"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="export" value="METABOLITE"/> - <param name="db" value="metanetx.chemical"/> - <param name="skip" value="true"/> - <param name="uniq" value="true"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="111"/> - <has_n_columns n="2"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/ExtractSbmlAnnot/test-data/Human-GEM_pathways.xml --- a/tools/attributes/ExtractSbmlAnnot/test-data/Human-GEM_pathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,7661 +0,0 @@\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 1274e2a62479 -r 0976a6257300 tools/attributes/GetEntities/GetEntities.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/GetEntities/GetEntities.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,198 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_GetEntities" name="GetEntities" version="develop"> + <description>Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetEntities -i "$sbml" + $printMetabolites + $printReactions + $printCompartments + $printPathways + $printGenes + $noTypeCol + -o "$outputFile" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-m" checked="false" falsevalue="" label="Extract Metabolites" name="printMetabolites" truevalue="-m" type="boolean" value="false"/> + <param argument="-r" checked="false" falsevalue="" label="Extract Reactions" name="printReactions" truevalue="-r" type="boolean" value="false"/> + <param argument="-c" checked="false" falsevalue="" label="Extract Compartments" name="printCompartments" truevalue="-c" type="boolean" value="false"/> + <param argument="-p" checked="false" falsevalue="" label="Extract Pathways" name="printPathways" truevalue="-p" type="boolean" value="false"/> + <param argument="-g" checked="false" falsevalue="" label="Extract Genes" name="printGenes" truevalue="-g" type="boolean" value="false"/> + <param argument="-nt" checked="false" falsevalue="" label="Do not write type column" name="noTypeCol" truevalue="-nt" type="boolean" value="false"/> + </inputs> + <outputs> + <data format="tsv" name="outputFile"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="Human-GEM_pathways.xml"/> + + + + + + + <output ftype="tsv" name="outputFile"> + + + + + + + <assert_contents> + + + + + + + <has_text_matching expression="GENE" n="86"/> + + + + + + + <has_text_matching expression="METABOLITE" n="111"/> + + + + + + + <has_text_matching expression="REACTION" n="75"/> + + + + + + + <has_text_matching expression="PATHWAY" n="3"/> + + + + + + + <has_text_matching expression="COMPARTMENT" n="5"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test> + + + + + + + <param name="sbml" value="Human-GEM_pathways.xml"/> + + + + + + + <param name="printReactions" value="true"/> + + + + + + + <param name="printMetabolites" value="true"/> + + + + + + + <param name="printGenes" value="true"/> + + + + + + + <param name="printCompartments" value="true"/> + + + + + + + <param name="noTypeCol" value="true"/> + + + + + + + <output ftype="tsv" name="outputFile"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="277"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.The output file is a tabulated file with two columns, one with entity identifiers, and one with the entity type. If no entity type is selected, all of them are returned by default. Only identifiers are written, attributes can be extracted from dedicated apps or from the Sbml2Tab app.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/GetEntities/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/GetEntities/test-data/Human-GEM_pathways.xml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml --- a/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="MET4J_VERSION_TEST"> - <description>Get gene lists from a list of reactions and a GSMN.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="develop"> + <description>Get gene lists from a list of reactions and 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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml" -r "$reactionFile" @@ -34,17 +34,127 @@ </outputs> <tests> <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="reactionFile" value="XF_network_R_Seed.tab"/> - <output ftype="tsv" name="outputFile"> - <assert_contents> - <has_n_lines n="2"/> - <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> - <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> - </assert_contents> - </output> - </test> + + + + + + + + + + + + <param name="sbml" value="XF_network.sbml"/> + + + + + + + + + + + + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + + + + + + + + + + + + <output ftype="tsv" name="outputFile"> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <has_n_lines n="2"/> + + + + + + + + + + + + <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> + + + + + + + + + + + + <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + + </test> </tests> - <help><![CDATA[Get associated gene list from a list of reactions and a GSMN. Parse GSMN GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help> + <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help> <citations/> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,94 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetMetaboliteAttributes -i "$sbml" + -o "$outputFile" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/> + </inputs> + <outputs> + <data format="tsv" name="outputFile"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <output ftype="tsv" name="outputFile"> + + + + + + + <assert_contents> + + + + + + + <has_n_lines n="9"/> + + + + + + + <has_n_columns n="6"/> + + + + + + + <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/> + + + + + + + <has_line_matching expression=".*C.*NC.*" n="1"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/GetMetaboliteAttributes/test-data/tests.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/GetMetaboliteAttributes/test-data/tests.tsv Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,9 @@ +id name formula charge smiles inchi +A A null 0 null null +B B null 0 null null +A_ext A_ext null 0 C[C@@H](C(=O)O)NC 1S/C2H6O/c1-2-3/h3H,2H2,1H3 +C C null 0 null null +D D null 0 null null +E E null 0 null null +D_ext D_ext null 0 null null +E_ext E_ext null 0 null null |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/GetMetaboliteAttributes/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/GetMetaboliteAttributes/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml --- a/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="MET4J_VERSION_TEST">\n- <description>Get reactants lists from a list of reactions and a GSMN.</description>\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="develop">\n+ <description>Get reactant lists from a list of reactions and a SBML file.</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetReactantsFromReactions -i "$sbml"\n -r "$reactionFile"\n@@ -38,38 +38,357 @@\n </outputs>\n <tests>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="sbml" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="reactionFile" value="XF_network_R_Seed.tab"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="tsv" name="outputFile">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_GLUN" n="4"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_ACGS" n="5"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="sbml" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="reactionFile" value="XF_network_R_Seed.tab"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="printSubstrates" value="true"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="tsv" name="outputFile">\n+ '..b' \n+ \n <has_text_matching expression="R_GLUN" n="2"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_ACGS" n="5"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="sbml" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="reactionFile" value="XF_network_R_Seed.tab"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="printProducts" value="true"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="tsv" name="outputFile">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_GLUN" n="2"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_text_matching expression="R_ACGS" n="5"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n- <help><![CDATA[Get reactants lists from a list of reactions and a GSMN. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered both substrates and products]]></help>\n+ <help><![CDATA[Get reactant lists from a list of reactions and a Sbml file. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered as both substrates and products]]></help>\n <citations/>\n </tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml --- a/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan': - -cc "$colcharge" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p - $s -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="charges.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="chargesWithComment.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="charges.tsv"/> - <param name="nSkip" value="1"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="charges.tsv"/> - <param name="ci" value="2"/> - <param name="cc" value="3"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="chargesXF.tsv"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas -The charge must be a number. The ids must correspond between the tabulated file and the SBML file. -If prefix or suffix is different in the SBML file, use the -p or the -s options. -The charge will be written in the SBML file in two locations:+ -- in the reaction notes (e.g. <p>charge: -1</p>) -- as fbc attribute (e.g. fbc:charge="1")]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetChargesFromFile/test-data/XF_network.sbml --- a/tools/attributes/SbmlSetChargesFromFile/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetChargesFromFile/test-data/charges.tsv --- a/tools/attributes/SbmlSetChargesFromFile/test-data/charges.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A 2 -B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetChargesFromFile/test-data/chargesDifferentColumns.tsv --- a/tools/attributes/SbmlSetChargesFromFile/test-data/chargesDifferentColumns.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Line1 A 2 -Line2 B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetChargesFromFile/test-data/chargesWithComment.tsv --- a/tools/attributes/SbmlSetChargesFromFile/test-data/chargesWithComment.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#A 2 -B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetChargesFromFile/test-data/chargesXF.tsv --- a/tools/attributes/SbmlSetChargesFromFile/test-data/chargesXF.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -glc_D -1000 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetChargesFromFile/test-data/toy_model.xml --- a/tools/attributes/SbmlSetChargesFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml --- a/tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,73 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetEcsFromFile#if str($colec) != 'nan': - -cec "$colec" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cec" label="[2] number of the column where are the ecs" name="colec" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="ec.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*1.1.1.1.*" n="2"/> - <has_line_matching expression=".*1.2.3.4.*" n="2"/> - </assert_contents> - </output> - </test> - <test expect_failure="true"> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="ecBad.tsv"/> - </test> - </tests> - <help><![CDATA[Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC -The ids must correspond between the tabulated file and the SBML file. -If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. -The EC will be written in the SBML file in two locations: -- in the reaction notes (e.g. <p>EC_NUMBER: 2.4.2.14</p>) -- as a reaction annotation (e.g. <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/>)]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetEcsFromFile/test-data/ec.tsv --- a/tools/attributes/SbmlSetEcsFromFile/test-data/ec.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 1.1.1.1 -reac2 1.2.3.4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetEcsFromFile/test-data/ecBad.tsv --- a/tools/attributes/SbmlSetEcsFromFile/test-data/ecBad.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 1.1.1.1 -reac2 1.2.3.4.5 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetEcsFromFile/test-data/toy_model.xml --- a/tools/attributes/SbmlSetEcsFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml --- a/tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,76 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan': - -cf "$colformula" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p - $s -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cf" label="[2] number of the column where are the formulas" name="colformula" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="formula.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*CH6O6.*" n="2"/> - <has_line_matching expression=".*CH12O4.*" n="2"/> - </assert_contents> - </output> - </test> - <test expect_failure="true"> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="formulaBad.tsv"/> - </test> - </tests> - <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas -The ids must correspond between the tabulated file and the SBML file. -If prefix or suffix is different in the SBML file, use the -p or the -s options. -The formula will be written in the SBML file in two locations:+ -- in the metabolite notes (e.g. <p>formula: C16H29O2</p> - -- as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetFormulasFromFile/test-data/formula.tsv --- a/tools/attributes/SbmlSetFormulasFromFile/test-data/formula.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A CH6O6 -B CH12O4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetFormulasFromFile/test-data/formulaBad.tsv --- a/tools/attributes/SbmlSetFormulasFromFile/test-data/formulaBad.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A CH6O6 -B 12CH4O \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetFormulasFromFile/test-data/toy_model.xml --- a/tools/attributes/SbmlSetFormulasFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml --- a/tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,83 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan': - -cgpr "$colgpr" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cgpr" label="[2] number of the column where are the gprs" name="colgpr" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="gpr.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> - <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> - <has_line_matching expression=".*fbc:id=.G3.*" n="1"/> - <has_line_matching expression=".*fbc:id=.G4.*" n="1"/> - <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/> - <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/> - <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/> - <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/> - <has_line_matching expression=".*fbc:and.*" n="2"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[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 -The ids must correspond between the tabulated file and the SBML file. -If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. -GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307 -(The GPR will be written in the SBML file in two locations: -- in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p> -- as fbc gene product association :<fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="XC_3282"/> - <fbc:geneProductRef fbc:geneProduct="XC_0401"/> - </fbc:or> -</fbc:geneProductAssociation> -]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetGprsFromFile/test-data/gpr.tsv --- a/tools/attributes/SbmlSetGprsFromFile/test-data/gpr.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 G1 or G2 -reac2 G3 and G4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetGprsFromFile/test-data/gprBad.tsv --- a/tools/attributes/SbmlSetGprsFromFile/test-data/gprBad.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 G1 or G2 -reac2 G3 an G4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetGprsFromFile/test-data/toy_model.xml --- a/tools/attributes/SbmlSetGprsFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml --- a/tools/attributes/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,129 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetIdsFromFile" name="SbmlSetIdsFromFile" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetIdsFromFile#if str($colname) != 'nan': - -cnew "$colname" -#end if -#if str($colid): - -ci "$colid" -#end if - $p - $s -#if str($o): - -o "$o" -#end if -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="idMetabolites.tsv"/> - <param name="o" value="METABOLITE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*id=.metaboliteA.*" n="1"/> - <has_line_matching expression=".*id=.metaboliteB.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="idReactions.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*id=.reaction1.*" n="1"/> - <has_line_matching expression=".*id=.reaction2.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="idPathways.tsv"/> - <param name="o" value="PATHWAY"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*groups:id=.CEB.*" n="1"/> - <has_line_matching expression=".*groups:id=.NSP.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="idGenes.tsv"/> - <param name="o" value="GENE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> - <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="idCompartments.tsv"/> - <param name="o" value="COMPARTMENT"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*id=.cytosol.*" n="1"/> - <has_line_matching expression=".*id=.extra.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Set new ids to network objects from a tabulated file containing the old ids and the new ids -The ids must correspond between the tabulated file and the SBML file. -If prefix or suffix is different in the SBML file, use the -p or the -s options. -]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetIdsFromFile/test-data/XF_network.sbml --- a/tools/attributes/SbmlSetIdsFromFile/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetIdsFromFile/test-data/idCompartments.tsv --- a/tools/attributes/SbmlSetIdsFromFile/test-data/idCompartments.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -c cytosol -e extra \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetIdsFromFile/test-data/idGenes.tsv --- a/tools/attributes/SbmlSetIdsFromFile/test-data/idGenes.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -XFCFBP8418_007090 G1 -XFCFBP8418_005900 G2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetIdsFromFile/test-data/idMetabolites.tsv --- a/tools/attributes/SbmlSetIdsFromFile/test-data/idMetabolites.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A metaboliteA -B metaboliteB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetIdsFromFile/test-data/idPathways.tsv --- a/tools/attributes/SbmlSetIdsFromFile/test-data/idPathways.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Nucleotide_Salvage_Pathway NSP -Cell_Envelope_Biosynthesis CEB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetIdsFromFile/test-data/idReactions.tsv --- a/tools/attributes/SbmlSetIdsFromFile/test-data/idReactions.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 reaction1 -reac2 reaction2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetIdsFromFile/test-data/toy_model.xml --- a/tools/attributes/SbmlSetIdsFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml --- a/tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,117 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetNamesFromFile#if str($colname) != 'nan': - -cname "$colname" -#end if -#if str($colid): - -ci "$colid" -#end if - $p - $s -#if str($o): - -o "$o" -#end if -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cname" label="[2] number of the column where are the names" name="colname" optional="true" type="integer" value="2"/> - <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="namesMetabolites.tsv"/> - <param name="o" value="METABOLITE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*metaboliteA.*" n="1"/> - <has_line_matching expression=".*metaboliteB.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="namesReactions.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*reaction1.*" n="1"/> - <has_line_matching expression=".*reaction2.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="namesPathways.tsv"/> - <param name="o" value="PATHWAY"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*groups:name=.CEB.*" n="1"/> - <has_line_matching expression=".*groups:name=.NSP.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="namesGenes.tsv"/> - <param name="o" value="GENE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:name=.G1.*" n="1"/> - <has_line_matching expression=".*fbc:name=.G2.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Set names to network objects from a tabulated file containing the object ids and the names -The ids must correspond between the tabulated file and the SBML file. -If prefix or suffix is different in the SBML file, use the -p or the -s options. -]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetNamesFromFile/test-data/XF_network.sbml --- a/tools/attributes/SbmlSetNamesFromFile/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetNamesFromFile/test-data/namesGenes.tsv --- a/tools/attributes/SbmlSetNamesFromFile/test-data/namesGenes.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -XFCFBP8418_007090 G1 -XFCFBP8418_005900 G2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetNamesFromFile/test-data/namesMetabolites.tsv --- a/tools/attributes/SbmlSetNamesFromFile/test-data/namesMetabolites.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A metaboliteA -B metaboliteB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetNamesFromFile/test-data/namesPathways.tsv --- a/tools/attributes/SbmlSetNamesFromFile/test-data/namesPathways.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Nucleotide_Salvage_Pathway NSP -Cell_Envelope_Biosynthesis CEB |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetNamesFromFile/test-data/namesReactions.tsv --- a/tools/attributes/SbmlSetNamesFromFile/test-data/namesReactions.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -reac1 reaction1 -reac2 reaction2 |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetNamesFromFile/test-data/toy_model.xml --- a/tools/attributes/SbmlSetNamesFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml --- a/tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,97 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan': - -cp "$colp" -#end if -#if str($sep): - -sep "$sep" -#end if -#if str($colid) != 'nan': - -ci "$colid" -#end if - $p -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cp" label="[2] number of the column where are the pathways" name="colp" optional="true" type="integer" value="2"/> - <param argument="-sep" label="[|] Separator of pathways in the tabulated file" name="sep" optional="true" type="text" value="|"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="pathways.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*groups:id=.*" n="3"/> - <has_line_matching expression=".*groups:id=.p1.*" n="1"/> - <has_line_matching expression=".*groups:id=.p2.*" n="1"/> - <has_line_matching expression=".*groups:id=.p3.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="pathwaysOtherSep.tsv"/> - <param name="sep" value=" + "/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*groups:id=.*" n="3"/> - <has_line_matching expression=".*groups:id=.p1.*" n="1"/> - <has_line_matching expression=".*groups:id=.p2.*" n="1"/> - <has_line_matching expression=".*groups:id=.p3.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways -The ids must correspond between the tabulated file and the SBML file. -If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. -Pathways will be written in the SBML file in two ways:- as reaction note (e.g. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group: -<groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis"> - <groups:listOfMembers> - <groups:member groups:idRef="R_GLUPRT"/> - <groups:member groups:idRef="R_RNDR1b"/> -... -]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetPathwaysFromFile/test-data/pathways.tsv --- a/tools/attributes/SbmlSetPathwaysFromFile/test-data/pathways.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -reac1 P1 -reac2 P2|P3 -reac3 P1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetPathwaysFromFile/test-data/pathwaysOtherSep.tsv --- a/tools/attributes/SbmlSetPathwaysFromFile/test-data/pathwaysOtherSep.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -reac1 P1 -reac2 P2 + P3 -reac3 P1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetPathwaysFromFile/test-data/toy_model.xml --- a/tools/attributes/SbmlSetPathwaysFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml --- a/tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,88 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan': - -cr "$colRef" -#end if - -ref "$ref" -#if str($colid): - -ci "$colid" -#end if - $p - $s -#if str($o): - -o "$o" -#end if -#if str($nSkip): - -n "$nSkip" -#end if - -sbml "$sbml" -#if str($tab) != 'None': - -tab "$tab" -#end if -#if str($c): - -c "$c" -#end if - -out "$out" -]]></command> - <inputs> - <param argument="-cr" label="[2] number of the column where are the references" name="colRef" optional="true" type="integer" value="2"/> - <param argument="-ref" label="Name of the ref. Must exist in identifiers.org" name="ref" optional="false" type="text" value=""> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/> - <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> - <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> - <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> - <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="sbml" name="out"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="refs.tsv"/> - <param name="ref" value="InChi"/> - <param name="o" value="METABOLITE"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*C2H6O.*" n="3"/> - <has_line_matching expression=".*C6H8O6.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Add refs to network objects from a tabulated file containing the metabolite ids and the formulas -Reference name given as parameter (-ref) must correspond to an existing id the registry of identifiers.org (https://registry.identifiers.org/registry) -The corresponding key:value pair will be written as metabolite or reaction annotation]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetRefsFromFile/test-data/refs.tsv --- a/tools/attributes/SbmlSetRefsFromFile/test-data/refs.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -A InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 -B InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-8,10-11H,1H2/t2-,5+/m0/s1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlSetRefsFromFile/test-data/toy_model.xml --- a/tools/attributes/SbmlSetRefsFromFile/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml --- a/tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,34 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlToMetaboliteTable -s "$sbml" - -o "$outputFile" -]]></command> - <inputs> - <param argument="-s" format="sbml" label="Sbml file" name="sbml" optional="false" type="data" value=""/> - </inputs> - <outputs> - <data format="tsv" name="outputFile"/> - </outputs> - <tests> - <test> - <param name="sbml" value="toy_model.xml"/> - <output ftype="tsv" name="outputFile"> - <assert_contents> - <has_n_lines n="9"/> - <has_n_columns n="6"/> - <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/> - <has_line_matching expression=".*C.*NC.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlToMetaboliteTable/test-data/tests.tsv --- a/tools/attributes/SbmlToMetaboliteTable/test-data/tests.tsv Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,9 +0,0 @@ -id name formula charge smiles inchi -A A null 0 null null -B B null 0 null null -A_ext A_ext null 0 C[C@@H](C(=O)O)NC 1S/C2H6O/c1-2-3/h3H,2H2,1H3 -C C null 0 null null -D D null 0 null null -E E null 0 null null -D_ext D_ext null 0 null null -E_ext E_ext null 0 null null |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SbmlToMetaboliteTable/test-data/toy_model.xml --- a/tools/attributes/SbmlToMetaboliteTable/test-data/toy_model.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -<?xml version="1.0" encoding='UTF-8' ?> -<sbml fbc:required="false" groups:required="false" level="3" version="1" - xmlns="http://www.sbml.org/sbml/level3/version1/core" - xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" - xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" name="toy model"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="false" id="c" name="Cytosol"/> - <compartment constant="false" id="e" name="Extracellular"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> - <notes> - <body xmlns="http://www.w3.org/1999/xhtml"> - <p>SMILES: C[C@@H](C(=O)O)NC</p> - </body> - </notes> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#A_ext"> - <bqbiol:is> - <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - - </species> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> - <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> - <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> - <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> - <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> - <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> - </listOfParameters> - <listOfReactions> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="A" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="B" stoichiometry="1.0"/> - <speciesReference constant="true" species="C" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.5"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="E" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> - <listOfReactants> - <speciesReference constant="true" species="E" stoichiometry="2.0"/> - </listOfReactants> - <listOfProducts> - <speciesReference constant="true" species="D" stoichiometry="1.0"/> - </listOfProducts> - </reaction> - </listOfReactions> - </model> -</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetCharges/SetCharges.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetCharges/SetCharges.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -0,0 +1,445 @@\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SetCharges" name="SetCharges" version="develop">\n+ <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</description>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetCharges#if str($colcharge) != \'nan\':\n+ -cc "$colcharge"\n+#end if\n+#if str($colid) != \'nan\':\n+ -ci "$colid"\n+#end if\n+ $p\n+ $s\n+#if str($nSkip):\n+ -n "$nSkip"\n+#end if\n+ -i "$sbml"\n+#if str($tab) != \'None\':\n+ -tab "$tab"\n+#end if\n+#if str($c):\n+ -c "$c"\n+#end if\n+ -o "$out"\n+]]></command>\n+ <inputs>\n+ <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" optional="true" type="integer" value="2"/>\n+ <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/>\n+ <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/>\n+ <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>\n+ <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>\n+ <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>\n+ <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won\'t be read" name="c" optional="true" type="text" value="#">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data format="sbml" name="out"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="toy_model.xml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="charges.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param na'..b' \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="toy_model.xml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="charges.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="ci" value="2"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="cc" value="3"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="chargesXF.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="p" value="true"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="s" value="true"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges\n+The charge must be a number. The ids must correspond between the tabulated file and the SBML file.\n+If prefix or suffix is different in the SBML file, use the -p or the -s options.\n+The charge will be written in the SBML file in two locations:+\n+- in the reaction notes (e.g. charge: -1)\n+- as fbc attribute (e.g. fbc:charge="1")]]></help>\n+ <citations>\n+ <citation type="doi">10.1515/jib-2017-0082</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetCharges/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetCharges/test-data/XF_network.sbml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 tools/attributes/SetCharges/test-data/charges.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetCharges/test-data/charges.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A 2 +B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetCharges/test-data/chargesDifferentColumns.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetCharges/test-data/chargesDifferentColumns.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Line1 A 2 +Line2 B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetCharges/test-data/chargesWithComment.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetCharges/test-data/chargesWithComment.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#A 2 +B -3 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetCharges/test-data/chargesXF.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetCharges/test-data/chargesXF.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,1 @@ +glc_D -1000 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetCharges/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetCharges/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetChemicalFormulas/SetChemicalFormulas.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetChemicalFormulas/SetChemicalFormulas.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,155 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetChemicalFormulas#if str($colformula) != 'nan': + -cf "$colformula" +#end if +#if str($colid) != 'nan': + -ci "$colid" +#end if + $p + $s +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cf" label="[2] number of the column where are the formulas" name="colformula" optional="true" type="integer" value="2"/> + <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="formula.tsv"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*CH6O6.*" n="2"/> + + + + + + + <has_line_matching expression=".*CH12O4.*" n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test expect_failure="true"> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="formulaBad.tsv"/> + + + + + + + </test> + </tests> + <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas +The ids must correspond between the tabulated file and the SBML file. +If prefix or suffix is different in the SBML file, use the -p or the -s options. +The formula will be written in the SBML file in two locations:+ +- in the metabolite HTML notes (e.g. formula: C16H29O2) +- as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")]]></help> + <citations> + <citation type="doi">10.1515/jib-2017-0082</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetChemicalFormulas/test-data/formula.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetChemicalFormulas/test-data/formula.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A CH6O6 +B CH12O4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetChemicalFormulas/test-data/formulaBad.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetChemicalFormulas/test-data/formulaBad.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A CH6O6 +B 12CH4O \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetChemicalFormulas/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetChemicalFormulas/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetEcNumbers/SetEcNumbers.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetEcNumbers/SetEcNumbers.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,153 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetEcNumbers" name="SetEcNumbers" version="develop"> + <description>Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetEcNumbers#if str($colec) != 'nan': + -cec "$colec" +#end if +#if str($colid) != 'nan': + -ci "$colid" +#end if + $p +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cec" label="[2] number of the column where are the ecs" name="colec" optional="true" type="integer" value="2"/> + <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="ec.tsv"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*1.1.1.1.*" n="2"/> + + + + + + + <has_line_matching expression=".*1.2.3.4.*" n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test expect_failure="true"> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="ecBad.tsv"/> + + + + + + + </test> + </tests> + <help><![CDATA[Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers +The ids must correspond between the tabulated file and the SBML file. +If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. +The EC will be written in the SBML file in two locations: +- in the reaction HTML notes (e.g. EC_NUMBER: 2.4.2.14) +- as a reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/) with ec-code identifiers link (https://registry.identifiers.org/registry/ec-code)]]></help> + <citations> + <citation type="doi">10.1038/nbt1156</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetEcNumbers/test-data/ec.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetEcNumbers/test-data/ec.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 1.1.1.1 +reac2 1.2.3.4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetEcNumbers/test-data/ecBad.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetEcNumbers/test-data/ecBad.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 1.1.1.1 +reac2 1.2.3.4.5 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetEcNumbers/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetEcNumbers/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetGprs/SetGprs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetGprs/SetGprs.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,182 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetGprs" name="SetGprs" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetGprs#if str($colgpr) != 'nan': + -cgpr "$colgpr" +#end if +#if str($colid) != 'nan': + -ci "$colid" +#end if + $p +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cgpr" label="[2] number of the column where are the gprs" name="colgpr" optional="true" type="integer" value="2"/> + <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="gpr.tsv"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:id=.G3.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:id=.G4.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/> + + + + + + + <has_line_matching expression=".*fbc:and.*" n="2"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[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 +The ids must correspond between the tabulated file and the SBML file. +If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. +GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307 +(The GPR will be written in the SBML file in two locations: +- in the reaction html notes (GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )) +- as fbc gene product association (see FBC package specifications: https://doi.org/10.1515/jib-2017-0082)]]></help> + <citations> + <citation type="doi">10.1038/nprot.2011.308</citation> + <citation type="doi">10.1515/jib-2017-0082</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetGprs/test-data/gpr.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetGprs/test-data/gpr.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 G1 or G2 +reac2 G3 and G4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetGprs/test-data/gprBad.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetGprs/test-data/gprBad.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 G1 or G2 +reac2 G3 an G4 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetGprs/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetGprs/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetIds/SetIds.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetIds/SetIds.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -0,0 +1,453 @@\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SetIds" name="SetIds" version="develop">\n+ <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</description>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetIds#if str($colname) != \'nan\':\n+ -cnew "$colname"\n+#end if\n+#if str($colid):\n+ -ci "$colid"\n+#end if\n+ $p\n+ $s\n+#if str($o):\n+ -t "$o"\n+#end if\n+#if str($nSkip):\n+ -n "$nSkip"\n+#end if\n+ -i "$sbml"\n+#if str($tab) != \'None\':\n+ -tab "$tab"\n+#end if\n+#if str($c):\n+ -c "$c"\n+#end if\n+ -o "$out"\n+]]></command>\n+ <inputs>\n+ <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/>\n+ <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>\n+ <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>\n+ <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>\n+ <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>\n+ <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won\'t be read" name="c" optional="true" type="text" value="#">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data format="sbml" name="out"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="toy_model.xml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="idMetabolites.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="METABOLITE"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ '..b'+ \n+ <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="idGenes.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="GENE"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="idCompartments.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="COMPARTMENT"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*id=.cytosol.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*id=.extra.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids\n+The ids must correspond between the tabulated file and the SBML file.\n+If prefix or suffix is different in the SBML file, use the -p or the -s options.\n+]]></help>\n+ <citations/>\n+</tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetIds/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetIds/test-data/XF_network.sbml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 tools/attributes/SetIds/test-data/idCompartments.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetIds/test-data/idCompartments.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +c cytosol +e extra \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetIds/test-data/idGenes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetIds/test-data/idGenes.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +XFCFBP8418_007090 G1 +XFCFBP8418_005900 G2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetIds/test-data/idMetabolites.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetIds/test-data/idMetabolites.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A metaboliteA +B metaboliteB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetIds/test-data/idPathways.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetIds/test-data/idPathways.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Nucleotide_Salvage_Pathway NSP +Cell_Envelope_Biosynthesis CEB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetIds/test-data/idReactions.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetIds/test-data/idReactions.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 reaction1 +reac2 reaction2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetIds/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetIds/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetNames/SetNames.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetNames/SetNames.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -0,0 +1,375 @@\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SetNames" name="SetNames" version="develop">\n+ <description>Set names to network objects in a SBML file from a tabulated file containing the object ids and the names</description>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetNames#if str($colname) != \'nan\':\n+ -cname "$colname"\n+#end if\n+#if str($colid):\n+ -ci "$colid"\n+#end if\n+ $p\n+ $s\n+#if str($o):\n+ -t "$o"\n+#end if\n+#if str($nSkip):\n+ -n "$nSkip"\n+#end if\n+ -i "$sbml"\n+#if str($tab) != \'None\':\n+ -tab "$tab"\n+#end if\n+#if str($c):\n+ -c "$c"\n+#end if\n+ -o "$out"\n+]]></command>\n+ <inputs>\n+ <param argument="-cname" label="[2] number of the column where are the names" name="colname" optional="true" type="integer" value="2"/>\n+ <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>\n+ <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>\n+ <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>\n+ <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>\n+ <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won\'t be read" name="c" optional="true" type="text" value="#">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data format="sbml" name="out"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="toy_model.xml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="namesMetabolites.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="METABOLITE"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*metaboliteA.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ '..b' \n+ <has_line_matching expression=".*reaction1.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*reaction2.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="namesPathways.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="PATHWAY"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*groups:name=.CEB.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*groups:name=.NSP.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="tab" value="namesGenes.tsv"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <param name="o" value="GENE"/>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <output ftype="sbml" name="out">\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <is_valid_xml/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:name=.G1.*" n="1"/>\n+ \t\t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ <has_line_matching expression=".*fbc:name=.G2.*" n="1"/>\n+ \t\t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \t\t\t\n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \t\t\n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Set names to network objects in a SBML file from a tabulated file containing the object ids and the names\n+The ids must correspond between the tabulated file and the SBML file.\n+If prefix or suffix is different in the SBML file, use the -p or the -s options.\n+]]></help>\n+ <citations/>\n+</tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetNames/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetNames/test-data/XF_network.sbml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 tools/attributes/SetNames/test-data/namesGenes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetNames/test-data/namesGenes.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +XFCFBP8418_007090 G1 +XFCFBP8418_005900 G2 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetNames/test-data/namesMetabolites.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetNames/test-data/namesMetabolites.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A metaboliteA +B metaboliteB \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetNames/test-data/namesPathways.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetNames/test-data/namesPathways.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Nucleotide_Salvage_Pathway NSP +Cell_Envelope_Biosynthesis CEB |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetNames/test-data/namesReactions.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetNames/test-data/namesReactions.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +reac1 reaction1 +reac2 reaction2 |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetNames/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetNames/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetPathways/SetPathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetPathways/SetPathways.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,243 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetPathways" name="SetPathways" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetPathways#if str($colp) != 'nan': + -cp "$colp" +#end if +#if str($sep): + -sep "$sep" +#end if +#if str($colid) != 'nan': + -ci "$colid" +#end if + $p +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cp" label="[2] number of the column where are the pathways" name="colp" optional="true" type="integer" value="2"/> + <param argument="-sep" label="[|] Separator of pathways in the tabulated file" name="sep" optional="true" type="text" value="|"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="pathways.tsv"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*groups:id=.*" n="3"/> + + + + + + + <has_line_matching expression=".*groups:id=.p1.*" n="1"/> + + + + + + + <has_line_matching expression=".*groups:id=.p2.*" n="1"/> + + + + + + + <has_line_matching expression=".*groups:id=.p3.*" n="1"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="pathwaysOtherSep.tsv"/> + + + + + + + <param name="sep" value=" + "/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*groups:id=.*" n="3"/> + + + + + + + <has_line_matching expression=".*groups:id=.p1.*" n="1"/> + + + + + + + <has_line_matching expression=".*groups:id=.p2.*" n="1"/> + + + + + + + <has_line_matching expression=".*groups:id=.p3.*" n="1"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways +The ids must correspond between the tabulated file and the SBML file. +If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. +Pathways will be written in the SBML file in two ways:- as reaction note (e.g. SUBSYSTEM: purine_biosynthesis)- as SBML group (see Group package specifications: https://pmc.ncbi.nlm.nih.gov/articles/PMC5451322/)]]></help> + <citations> + <citation type="doi">10.1515/jib-2016-290</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetPathways/test-data/pathways.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetPathways/test-data/pathways.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,3 @@ +reac1 P1 +reac2 P2|P3 +reac3 P1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetPathways/test-data/pathwaysOtherSep.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetPathways/test-data/pathwaysOtherSep.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,3 @@ +reac1 P1 +reac2 P2 + P3 +reac3 P1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetPathways/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetPathways/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetReferences/SetReferences.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetReferences/SetReferences.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,162 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SetReferences" name="SetReferences" version="develop"> + <description>Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetReferences#if str($colRef) != 'nan': + -cr "$colRef" +#end if + -ref "$ref" +#if str($colid): + -ci "$colid" +#end if + $p + $s +#if str($o): + -t "$o" +#end if +#if str($nSkip): + -n "$nSkip" +#end if + -i "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -o "$out" +]]></command> + <inputs> + <param argument="-cr" label="[2] number of the column where are the references" name="colRef" optional="true" type="integer" value="2"/> + <param argument="-ref" label="Name of the reference. Must exist in identifiers.org (https://registry.identifiers.org/registry)" name="ref" optional="false" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> + <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + + + + + + + <param name="sbml" value="toy_model.xml"/> + + + + + + + <param name="tab" value="refs.tsv"/> + + + + + + + <param name="ref" value="InChi"/> + + + + + + + <param name="o" value="METABOLITE"/> + + + + + + + <output ftype="sbml" name="out"> + + + + + + + <assert_contents> + + + + + + + <is_valid_xml/> + + + + + + + <has_line_matching expression=".*C2H6O.*" n="3"/> + + + + + + + <has_line_matching expression=".*C6H8O6.*" n="1"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references +Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry) +The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)]]></help> + <citations> + <citation type="doi">10.1038/nbt1156</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetReferences/test-data/refs.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetReferences/test-data/refs.tsv Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +A InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 +B InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-8,10-11H,1H2/t2-,5+/m0/s1 \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/attributes/SetReferences/test-data/toy_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SetReferences/test-data/toy_model.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/bigg/GetBiggModelProteome/GetBiggModelProteome.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/bigg/GetBiggModelProteome/GetBiggModelProteome.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,79 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="develop"> + <description>Get proteome in fasta format of a model present in the BIGG database</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetBiggModelProteome -m "$modelId" + -o "$outputFile" +]]></command> + <inputs> + <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="fasta" name="outputFile"/> + </outputs> + <tests> + <test maxseconds="120"> + + + + + + + <param name="modelId" value="e_coli_core"/> + + + + + + + <output ftype="fasta" name="outputFile"> + + + + + + + <assert_contents> + + + + + + + <has_line_matching expression=".*name=.*" n="136"/> + + + + + + + </assert_contents> + + + + + + + </output> + + + + + + + </test> + </tests> + <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help> + <citations> + <citation type="doi">10.1093/nar/gkv1049</citation> + </citations> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/bigg/GetModelProteome/GetModelProteome.xml --- a/tools/bigg/GetModelProteome/GetModelProteome.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,35 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_GetModelProteome" name="GetModelProteome" version="MET4J_VERSION_TEST"> - <description>Get proteome in fasta format of a model present in BIGG</description> - <xrefs> - <xref type="bio.tools">met4j</xref> - </xrefs> - <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetModelProteome -m "$modelId" - -o "$outputFile" -]]></command> - <inputs> - <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="fasta" name="outputFile"/> - </outputs> - <tests> - <test maxseconds="120"> - <param name="modelId" value="e_coli_core"/> - <output ftype="fasta" name="outputFile"> - <assert_contents> - <has_line_matching expression=".*name=.*" n="136"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Get proteome in fasta format of a model present in BIGG]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/bigg/GetModelProteome/proteome.fas --- a/tools/bigg/GetModelProteome/proteome.fas Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1153 +0,0 @@\n->b0755 name=gpmA\n-MAVTKLVLVRHGESQWNKENRFTGWYDVDLSEKGVSEAKAAGKLLKEEGYSFDFAYTSVL\n-KRAIHTLWNVLDELDQAWLPVEKSWKLNERHYGALQGLNKAETAEKYGDEQVKQWRRGFA\n-VTPPELTKDDERYPGHDPRYAKLSEKELPLTESLALTIDRVIPYWNETILPRMKSGERVI\n-IAAHGNSLRALVKYLDNMSEEEILELNIPTGVPLVYEFDENFKPLKRYYLGNADEIAAKA\n-AAVANQGKAK\n->b0008 name=talB\n-MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRKLIDDAVAWAK\n-QQSNDRAQQIVDATDKLAVNIGLEILKLVPGRISTEVDARLSYDTEASIAKAKRLIKLYN\n-DAGISNDRILIKLASTWQGIRAAEQLEKEGINCNLTLLFSFAQARACAEAGVFLISPFVG\n-RILDWYKANTDKKEYAPAEDPGVVSVSEIYQYYKEHGYETVVMGASFRNIGEILELAGCD\n-RLTIAPALLKELAESEGAIERKLSYTGEVKARPARITESEFLWQHNQDPMAVDKLAEGIR\n-KFAIDQEKLEKMIGDLL\n->b3951 name=pflD\n-MTNRISRLKTALFANTREISLERALLYTASHRQTEGEPVILRRAKATAYILEHVEISIRD\n-EELIAGNRTVKPRAGIMSPEMDPYWLLKELDQFPTRPQDRFAISEEDKRIYREELFPYWE\n-KRSMKDFINGQMTDEVKAATNTQIFSINQTDKGQGHIIIDYPRLLNHGLGELVAQMQQHC\n-QQQPENHFYQAALLLLEASQKHILRYAELAETMAANCTDAQRREELLTIAEISRHNAQHK\n-PQTFWQACQLFWYMNIILQYESNASSLSLGRFDQYMLPFYQTSLTQGEDAAFLKELLESL\n-WVKCNDIVLLRSTSSARYFAGFPTGYTALLGGLTENGRSAVNVLSFLCLDAYQSVQLPQP\n-NLGVRTNALIDTPFLMKTAETIRFGTGIPQIFNDEVVVPAFLNRGVSLEDARDYSVVGCV\n-ELSIPGRTYGLHDIAMFNLLKVMEICLHENEGNAALTYEGLLEQIRAKISHYITLMVEGS\n-NICDIGHRDWAPVPLLSSFISDCLEKGRDITDGGARYNFSGVQGIGIANLSDSLHALKGM\n-VFEQQRLSFDELLSVLKANFATPEGEKVRARLINRFEKYGNDIDEVDNISAELLRHYCKE\n-VEKYQNPRGGYFTPGSYTVSAHVPLGSVVGATPDGRFAGEQLADGGLSPMLGQDAQGPTA\n-VLKSVSKLDNTLLSNGTLLNVKFTPATLEGEAGLRKLADFLRAFTQLKLQHIQFNVVNAD\n-TLREAQQRPQDYAGLVVRVAGYSAFFVELSKEIQDDIIRRTAHQL\n->b0723 name=sdhA\n-MKLPVREFDAVVIGAGGAGMRAALQISQSGQTCALLSKVFPTRSHTVSAQGGITVALGNT\n-HEDNWEWHMYDTVKGSDYIGDQDAIEYMCKTGPEAILELEHMGLPFSRLDDGRIYQRPFG\n-GQSKNFGGEQAARTAAAADRTGHALLHTLYQQNLKNHTTIFSEWYALDLVKNQDGAVVGC\n-TALCIETGEVVYFKARATVLATGGAGRIYQSTTNAHINTGDGVGMAIRAGVPVQDMEMWQ\n-FHPTGIAGAGVLVTEGCRGEGGYLLNKHGERFMERYAPNAKDLAGRDVVARSIMIEIREG\n-RGCDGPWGPHAKLKLDHLGKEVLESRLPGILELSRTFAHVDPVKEPIPVIPTCHYMMGGI\n-PTKVTGQALTVNEKGEDVVVPGLFAVGEIACVSVHGANRLGGNSLLDLVVFGRAAGLHLQ\n-ESIAEQGALRDASESDVEASLDRLNRWNNNRNGEDPVAIRKALQECMQHNFSVFREGDAM\n-AKGLEQLKVIRERLKNARLDDTSSEFNTQRVECLELDNLMETAYATAVSANFRTESRGAH\n-SRFDFPDRDDENWLCHSLYLPESESMTRRSVNMEPKLRPAFPPKIRTY\n->b1723 name=pfkB\n-MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFP\n-AGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQ\n-LEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGN\n-IELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQ\n-VVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDT\n-QKIYAYLSR\n->b3603 name=lldP\n-MNLWQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKM\n-PVANALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLI\n-VGFCFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVA\n-GQVTGIDSFEIGQMVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYL\n-SSNFIGPELPDIISSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVL\n-RAWTPFLFLTATVTLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAY\n-AAVFKFDWFSATGTAILFAALLSIVWLKMKPSDAISTFGSTLKELALPIYSIGMVLAFAF\n-ISNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGV\n-SDLLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCIVGVITT\n-LQAYVLTWMIP\n->b1818 name=manY\n-MEITTLQIVLVFIVACIAGMGSILDEFQFHRPLIACTLVGIVLGDMKTGIIIGGTLEMIA\n-LGWMNIGAAVAPDAALASIISTILVIAGHQSIGAGIALAIPLAAAGQVLTIIVRTITVAF\n-QHAADKAADNGNLTAISWIHVSSLFLQAMRVAIPAVIVALSVGTSEVQNMLNAIPEVVTN\n-GLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFTNFNLVALGVIGTVMAVLYIQ\n-LSPKYNRVAGAPAQAAGNNDLDNELD\n->b0722 name=sdhD\n-MVSNASALGRNGVHDFILVRATAIVLTLYIIYMVGFFATSGELTYEVWIGFFASAFTKVF\n-TLLALFSILIHAWIGMWQVLTDYVKPLALRLMLQLVIVVALVVYVIYGFVVVWGV\n->b3731 name=atpC\n-MAMTYHLDVVSAEQQMFSGLVEKIQVTGSEGELGIYPGHAPLLTAIKPGMIRIVKQHGHE\n-EFIYLSGGILEVQPGNVTVLADTAIRGQDLDEARAMEAKRKAEEHISSSHGDVDYAQASA\n-ELAKAIAQLRVIELTKKAM\n->b2280 name=nuoJ\n-MEFAFYICGLIAILATLRVITHTNPVHALLYLIISLLAISGVFFSLGAYFAGALEIIVYA\n-GAIMVLFVFVVMMLNLGGSEIEQERQWLKPQVWIGPAILSAIMLVVIVYAILGVNDQGID\n-GTPISAKAVGITLFGPYVLAVELASMLLLAGLVVAFHVGREERAGEVLSNRKDDSAKRKT\n-EEHA\n->b0767 name=pgl\n-MKQTVYIASPESQQIHVWNLNHEGALTLTQVVDVPGQVQPMVVSPDKRYLYVGVRPEFRV\n-LAYRIAPDDGALTFAAESALPGSPTHISTDHQGQFVFVGSYNAGNVSVTRLEDGLPVGVV\n-DVVEGLDGCHSANISPDNRTLWVPALKQDRICLFTVSDDGHLVAQD'..b'AETKDGRWYPEFFRINFSRCIFCGLCEEACPTTAIQLTPDF\n-EMGEYKRQDLVYEKEDLLISGPGKYPEYNFYRMAGMAIDGKDKGEAENEAKPIDVKSLLP\n->b4301 name=sgcE\n-MILHPSLASANPLHYGRELTALDNLDFGSLHLDIEDSSFINNITFGMKTVQAVARQTPHP\n-LSFHFMLARPQRWFNALAEIRPAWIFVHAETLDYPSETLTEIRHTGARAGLVFNPATPID\n-AWRYLASELDGVMVMTSEPDGQGQRFIPSMCEKIQKVRTAFPQTECWADGGITLAAAQQL\n-AAAGAQHMVIGRALFSSSDYRATLAQFATL\n->b2463 name=maeB\n-MDDQLKQSALDFHEFPVPGKIQVSPTKPLATQRDLALAYSPGVAAPCLEIEKDPLKAYKY\n-TARGNLVAVISNGTAVLGLGNIGALAGKPVMEGKGVLFKKFAGIDVFDIEVDELDPDKFI\n-EVVAALEPTFGGINLEDIKAPECFYIEQKLRERMNIPVFHDDQHGTAIISTAAILNGLRV\n-VEKNISDVRMVVSGAGAAAIACMNLLVALGLQKHNIVVCDSKGVIYQGREPNMAETKAAY\n-AVVDDGKRTLDDVIEGADIFLGCSGPKVLTQEMVKKMARAPMILALANPEPEILPPLAKE\n-VRPDAIICTGRSDYPNQVNNVLCFPFIFRGALDVGATAINEEMKLAAVRAIAELAHAEQS\n-EVVASAYGDQDLSFGPEYIIPKPFDPRLIVKIAPAVAKAAMESGVATRPIADFDVYIDKL\n-TEFVYKTNLFMKPIFSQARKAPKRVVLPEGEEARVLHATQELVTLGLAKPILIGRPNVIE\n-MRIQKLGLQIKAGVDFEIVNNESDPRFKEYWTEYFQIMKRRGVTQEQAQRALISNPTVIG\n-AIMVQRGEADAMICGTVGDYHEHFSVVKNVFGYRDGVHTAGAMNALLLPSGNTFIADTYV\n-NDEPDAEELAEITLMAAETVRRFGIEPRVALLSHSNFGSSDCPSSSKMRQALELVRERAP\n-ELMIDGEMHGDAALVEAIRNDRMPDSSLKGSANILVMPNMEAARISYNLLRVSSSEGVTV\n-GPVLMGVAKPVHVLTPIASVRRIVNMVALAVVEAQTQPL\n->b2133 name=dld\n-MSSMTTTDNKAFLNELARLVGSSHLLTDPAKTARYRKGFRSGQGDALAVVFPGSLLELWR\n-VLKACVTADKIILMQAANTGLTEGSTPNGNDYDRDVVIISTLRLDKLHVLGKGEQVLAYP\n-GTTLYSLEKALKPLGREPHSVIGSSCIGASVIGGICNNSGGSLVQRGPAYTEMSLFARIN\n-EDGKLTLVNHLGIDLGETPEQILSKLDDDRIKDDDVRHDGRHAHDYDYVHRVRDIEADTP\n-ARYNADPDRLFESSGCAGKLAVFAVRLDTFEAEKNQQVFYIGTNQPEVLTEIRRHILANF\n-ENLPVAGEYMHRDIYDIAEKYGKDTFLMIDKLGTDKMPFFFNLKGRTDAMLEKVKFFRPH\n-FTDRAMQKFGHLFPSHLPPRMKNWRDKYEHHLLLKMAGDGVGEAKSWLVDYFKQAEGDFF\n-VCTPEEGSKAFLHRFAAAGAAIRYQAVHSDEVEDILALDIALRRNDTEWYEHLPPEIDSQ\n-LVHKLYYGHFMCYVFHQDYIVKKGVDVHALKEQMLELLQQRGAQYPAEHNVGHLYKAPET\n-LQKFYRENDPTNSMNPGIGKTSKRKNWQEVE\n->b3612 name=gpmM\n-MLVSKKPMVLVILDGYGYREEQQDNAIFSAKTPVMDALWANRPHTLIDASGLEVGLPDRQ\n-MGNSEVGHVNLGAGRIVYQDLTRLDVEIKDRAFFANPVLTGAVDKAKNAGKAVHIMGLLS\n-AGGVHSHEDHIMAMVELAAERGAEKIYLHAFLDGRDTPPRSAESSLKKFEEKFAALGKGR\n-VASIIGRYYAMDRDNRWDRVEKAYDLLTLAQGEFQADTAVAGLQAAYARDENDEFVKATV\n-IRAEGQPDAAMEDGDALIFMNFRADRAREITRAFVNADFDGFARKKVVNVDFVMLTEYAA\n-DIKTAVAYPPASLVNTFGEWMAKNDKTQLRISETEKYAHVTFFFNGGVEESFKGEDRILI\n-NSPKVATYDLQPEMSSAELTEKLVAAIKSGKYDTIICNYPNGDMVGHTGVMEAAVKAVEA\n-LDHCVEEVAKAVESVGGQLLITADHGNAEQMRDPATGQAHTAHTNLPVPLIYVGDKNVKA\n-VEGGKLSDIAPTMLSLMGMEIPQEMTGKPLFIVE\n->b2287 name=nuoB\n-MDYTLTRIDPNGENDRYPLQKQEIVTDPLEQEVNKNVFMGKLNDMVNWGRKNSIWPYNFG\n-LSCCYVEMVTSFTAVHDVARFGAEVLRASPRQADLMVVAGTCFTKMAPVIQRLYDQMLEP\n-KWVISMGACANSGGMYDIYSVVQGVDKFIPVDVYIPGCPPRPEAYMQALMLLQESIGKER\n-RPLSWVVGDQGVYRANMQSERERKRGERIAVTNLRTPDEI\n->b3737 name=atpE\n-MENLNMDLLYMAAAVMMGLAAIGAAIGIGILGGKFLEGAARQPDLIPLLRTQFFIVMGLV\n-DAIPMIAVGLGLYVMFAVA\n->b0810 name=glnP\n-MQFDWSAIWPAIPLLIEGAKMTLWISVLGLAGGLVIGLLAGFARTFGGWIANHVALVFIE\n-VIRGTPIVVQVMFIYFALPMAFNDLRIDPFTAAVVTIMINSGAYIAEITRGAVLSIHKGF\n-REAGLALGLSRWETIRYVILPLALRRMLPPLGNQWIISIKDTSLFIVIGVAELTRQGQEI\n-IAGNFRALEIWSAVAVFYLIITLVLSFILRRLERRMKIL\n->b0356 name=frmA\n-MKSRAAVAFAPGKPLEIVEIDVAPPKKGEVLIKVTHTGVCHTDAFTLSGDDPEGVFPVVL\n-GHEGAGVVVEVGEGVTSVKPGDHVIPLYTAECGECEFCRSGKTNLCVAVRETQGKGLMPD\n-GTTRFSYNGQPLYHYMGCSTFSEYTVVAEVSLAKINPEANHEHVCLLGCGVTTGIGAVHN\n-TAKVQPGDSVAVFGLGAIGLAVVQGARQAKAGRIIAIDTNPKKFDLARRFGATDCINPND\n-YDKPIKDVLLDINKWGIDHTFECIGNVNVMRAALESAHRGWGQSVIIGVAVAGQEISTRP\n-FQLVTGRVWKGSAFGGVKGRSQLPGMVEDAMKGDIDLEPFVTHTMSLDEINDAFDLMHEG\n-KSIRTVIRY\n->b2935 name=tktA\n-MSSRKELANAIRALSMDAVQKAKSGHPGAPMGMADIAEVLWRDFLKHNPQNPSWADRDRF\n-VLSNGHGSMLIYSLLHLTGYDLPMEELKNFRQLHSKTPGHPEVGYTAGVETTTGPLGQGI\n-ANAVGMAIAEKTLAAQFNRPGHDIVDHYTYAFMGDGCMMEGISHEVCSLAGTLKLGKLIA\n-FYDDNGISIDGHVEGWFTDDTAMRFEAYGWHVIRDIDGHDAASIKRAVEEARAVTDKPSL\n-LMCKTIIGFGSPNKAGTHDSHGAPLGDAEIALTREQLGWKYAPFEIPSEIYAQWDAKEAG\n-QAKESAWNEKFAAYAKAYPQEAAEFTRRMKGEMPSDFDAKAKEFIAKLQANPAKIASRKA\n-SQNAIEAFGPLLPEFLGGSADLAPSNLTLWSGSKAINEDAAGNYIHYGVREFGMTAIANG\n-ISLHGGFLPYTSTFLMFVEYARNAVRMAALMKQRQVMVYTHDSIGLGEDGPTHQPVEQVA\n-SLRVTPNMSTWRPCDQVESAVAWKYGVERQDGPTALILSRQNLAQQERTEEQLANIARGG\n-YVLKDCAGQPELIFIATGSEVELAVAAYEKLTAEGVKARVVSMPSTDAFDKQDAAYRESV\n-LPKAVTARVAVEAGIADYWYKYVGLNGAIVGMTTFGESAPAELLFEEFGFTVDNVVAKAK\n-ELL\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/FbcToNotes/FbcToNotes.xml --- a/tools/convert/FbcToNotes/FbcToNotes.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/convert/FbcToNotes/FbcToNotes.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,32 +1,122 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_FbcToNotes" name="FbcToNotes" version="MET4J_VERSION_TEST"> - <description>Convert FBC package annotations to sbml notes</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_FbcToNotes" name="FbcToNotes" version="develop"> + <description>Convert FBC package annotations to sbml html notes</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> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath" -o "$outputPath" ]]></command> <inputs> - <param argument="-i" format="sbml" label="input file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> </inputs> <outputs> <data format="sbml" name="outputPath"/> </outputs> <tests> <test> + + + + + + + + + + + <param name="inputPath" value="ECOL.xml"/> + + + + + + + + + + + <output ftype="sbml" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <is_valid_xml/> + + + + + + + + + + + <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> - <help><![CDATA[Convert FBC package annotations to sbml notes]]></help> - <citations/> + <help><![CDATA[Convert FBC package annotations to sbml html notes (see https://www.degruyter.com/document/doi/10.1515/jib-2017-0082/html)]]></help> + <citations> + <citation type="doi">10.1515/jib-2017-0082</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/Kegg2Sbml/Kegg2Sbml.xml --- a/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,16 +1,16 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="develop"> <description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org): -org "$org" #end if - -sbml "$sbml" + -o "$sbml" ]]></command> <inputs> <param argument="-org" label="[] Kegg org id. Must be 3 letters (" name="org" optional="true" type="text" value=""> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/SBMLwizard/SBMLwizard.xml --- a/tools/convert/SBMLwizard/SBMLwizard.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,79 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SBMLwizard" name="SBMLwizard" version="MET4J_VERSION_TEST"> - <description>General SBML model processing</description> - <xrefs> - <xref type="bio.tools">met4j</xref> - </xrefs> - <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SBMLwizard -s "$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 1274e2a62479 -r 0976a6257300 tools/convert/SBMLwizard/test-data/Human-GEM_pathways.xml --- a/tools/convert/SBMLwizard/test-data/Human-GEM_pathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,7661 +0,0 @@\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 1274e2a62479 -r 0976a6257300 tools/convert/SBMLwizard/test-data/XF_network.sbml --- a/tools/convert/SBMLwizard/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 tools/convert/SBMLwizard/test-data/XF_network_C_Side.tab --- a/tools/convert/SBMLwizard/test-data/XF_network_C_Side.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -M_atp_c -M_h2o_c -M_pi_c -M_adp_c -M_ppi_c -M_h_c |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/SBMLwizard/test-data/XF_network_R_Seed.tab --- a/tools/convert/SBMLwizard/test-data/XF_network_R_Seed.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -R_ACGS -R_GLUN |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -0,0 +1,371 @@\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="develop">\n+ <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>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CarbonSkeletonNet -i "$inputPath"\n+ -g "$inputAAM"\n+ $keepSingleCarbon\n+ $mergeComp\n+ $mergeEdges\n+ $removeIsolated\n+ $undirected\n+ $computeWeight\n+#if str($format):\n+ -f "$format"\n+#end if\n+ $main\n+ $fromIndexes\n+ -o "$output"\n+]]></command>\n+ <inputs>\n+ <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n+ <param argument="-g" format="gsam" label="input GSAM file" name="inputAAM" optional="false" type="data" value=""/>\n+ <param argument="-ks" checked="false" falsevalue="" label="keep edges involving single-carbon compounds, such as CO2 (requires formulas in SBML)" name="keepSingleCarbon" truevalue="-ks" type="boolean" value="false"/>\n+ <param argument="-mc" checked="false" falsevalue="" label="merge compartments (requires unique compound names that are consistent across compartments)" name="mergeComp" truevalue="-mc" type="boolean" value="false"/>\n+ <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>\n+ <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>\n+ <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>\n+ <param argument="-tp" checked="false" falsevalue="" label="set transition probability as weight" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>\n+ <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab">\n+ <option value="gml">gml</option>\n+ <option selected="true" value="tab">tab</option>\n+ <option value="nodeList">nodeList</option>\n+ <option value="json">json</option>\n+ <option value="matrix">matrix</option>\n+ </param>\n+ <param argument="-main" checked="false" falsevalue="" label="Compute RPAIRS-like tags and keep only main transitions for each reaction" name="main" truevalue="-main" type="boolean" value="false"/>\n+ <param argument="-fi" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-fi" type="boolean" value="false"/>\n+ </inputs>\n+ <outputs>\n+ <data format="txt" name="output"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \n+ \n+ \n+ <param name="inputPath" value="Human-GEM_pathways.xml"/>\n+ \n+ \n+ \n+ <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>\n+ \n+ \n+ \n+ <param name="format" value="gml"/>\n+ \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="2602"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ '..b' \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="2490"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \n+ \n+ \n+ <param name="inputPath" value="Human-GEM_pathways.xml"/>\n+ \n+ \n+ \n+ <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>\n+ \n+ \n+ \n+ <param name="undirected" value="true"/>\n+ \n+ \n+ \n+ <param name="format" value="gml"/>\n+ \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="3214"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \n+ \n+ \n+ <param name="inputPath" value="Human-GEM_pathways.xml"/>\n+ \n+ \n+ \n+ <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>\n+ \n+ \n+ \n+ <param name="format" value="matrix"/>\n+ \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="112"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ </test>\n+ <test>\n+ \n+ \n+ \n+ <param name="inputPath" value="Human-GEM_pathways.xml"/>\n+ \n+ \n+ \n+ <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/>\n+ \n+ \n+ \n+ <param name="fromIndexes" value="true"/>\n+ \n+ \n+ \n+ <param name="format" value="gml"/>\n+ \n+ \n+ \n+ <output name="output">\n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ <has_n_lines n="2611"/>\n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as \'biomass\' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produces a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) performs atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help>\n+ <citations/>\n+</tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab Fri Jan 31 18:28:53 2025 +0000 |
| b |
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|
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab Fri Jan 31 18:28:53 2025 +0000 |
| b |
| b'@@ -0,0 +1,206 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9-7-5-3-2\tR_RPEc\t2.8421709430404007E-14\t23,2,3,16,5,17,7,19,9,21\n+M_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tM_m01285c\t427.02941494\t30-28-26-24-22-21-19-17-15-14\tR_HMR_4402\t79.96633052199996\t22,24,14,26,15,28,17,19,30,21\n+M_m03130c\t483.96852767\t24-22-12-11-9-6-4-3-2\tM_m03106c\t404.002197148\t24-22-12-11-9-6-4-3-2\tR_HMR_4568\t79.96633052200002\t22,11,12,24,2,3,4,6,9\n+M_m01169c\t276.024633246\t39-37-35-33-31-29\tM_m01683c\t196.058302724\t39-37-35-33-31-29\tR_HMR_4476\t79.96633052200002\t33,35,37,39,29,31\n+M_m02332l\t342.116211524\t22-20-18-16-15-12-10-8-7-5-3-2\tM_m01965l\t370.147511652\t27-22-20-18-16-15-26-12-10-8-7-5-3-2\tR_HMR_8764\t28.031300127999998\t22,12,15,16,18,2,3,5,7,8,20,10\n+M_m01690c\t169.99802457399997\t5-3-2\tM_m01842c\t260.029718626\t5-15-3-12-13-2\tR_HMR_4356\t90.031694052\t2,3,5\n+M_m02883c\t370.00661383199997\t42-40-38-36-34-28-27\tM_m02884c\t290.04028331\t42-40-38-36-34-28-27\tR_HMR_4568\t79.96633052199996\t34,36,38,27,28,40,42\n+M_m03130c\t483.96852767\t28-26-12-11-9-6-4-3-2\tM_m03107c\t566.055020568\t28-26-44-42-40-38-37-35-12-11-9-6-4-3-2\tR_HMR_8767\t82.08649289800002\t11,12,26,28,2,3,4,6,9\n+M_m01939c\t169.998024574\t9-7-5\tM_m01761c\t230.019153942\t9-7-5-3-2\tR_HMR_4501\t60.021129368000004\t5,7,9\n+M_m02845c\t230.01915394199997\t9-7-5-3-2\tM_m02846c\t230.01915394199997\t9-7-5-3-2\tR_HMR_4352\t0.0\t2,3,5,7,9\n+M_m01909c\t182.07903816799998\t53-55-57-59-51-50\tM_m01910c\t180.06338810399998\t59-57-55-53-51-50\tR_HMR_8766\t2.015650063999999\t55,57,59,50,51,53\n+M_m01322c\t260.02971862600003\t44-42-40-38-37-35\tM_m03107c\t566.055020568\t28-26-44-42-40-38-37-35-12-11-9-6-4-3-2\tR_HMR_8767\t306.025301942\t44,35,37,38,40,42\n+M_m02372c\t244.034804006\t33-41-39-37-35-36\tM_m01159c\t164.06847348399998\t41-39-37-36-35-33\tR_HMR_4402\t79.96633052200002\t33,35,36,37,39,41\n+M_m01746c\t260.029718626\t32-44-42-36-34-31\tM_m02955c\t339.99604914799994\t44-42-36-34-32-31\tR_HMR_4774\t79.96633052199996\t44,34,36,42,31,32\n+M_m01910c\t180.06338810399998\t42-40-38-36-34-33\tM_m01911c\t260.029718626\t38-40-42-33-34-36\tR_HMR_4414\t79.96633052199999\t33,34,36,38,40,42\n+M_m01371c\t506.9'..b'5.09110239\t47-45-43-37-35-33-31-30-28-26-24-23-13-12-10-9-8-7-5-4-2\tR_HMR_4306\t1.0078250319999142\t33,45,23,12,35,24,13,47,37,26,28,2,4,5,7,8,9,30,31,43,10\n+M_m01371c\t506.99574546199995\t22-20-18-17-15-13-10-11-26-24\tM_m01285c\t427.02941494\t26-24-22-20-18-17-15-13-11-10\tR_HMR_4476\t79.96633052199996\t22,11,24,13,26,15,17,18,20,10\n+M_m02555c\t745.09110239\t47-45-43-37-35-33-31-30-28-26-24-23-13-12-10-9-8-7-5-4-2\tM_m02554c\t744.083277358\t47-45-43-37-35-33-31-30-28-26-24-23-13-12-10-9-8-7-5-4-2\tR_HMR_8766\t1.0078250319999142\t33,45,23,12,35,24,13,47,37,26,28,2,4,5,7,8,9,30,31,43,10\n+M_m02034c\t522.990660082\t46-44-30-29-27-25-23-22-20-18\tM_m01951c\t605.0771529799999\t44-46-25-23-18-20-22-27-29-30-15-13-11-9-8-6\tR_HMR_4387\t82.08649289799996\t44,22,23,46,25,27,18,29,30,20\n+M_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tM_m01334c\t347.063084418\t30-28-26-24-22-21-19-17-15-14\tR_HMR_4052\t159.93266104399993\t22,24,14,26,15,28,17,19,30,21\n+M_m02884c\t290.04028331\t42-40-38-36-34-28-27\tM_m02883c\t370.00661383199997\t42-40-38-36-34-28-27\tR_HMR_4568\t79.96633052199996\t34,36,38,27,28,40,42\n+M_m02552c\t664.116946836\t43-41-39-37-35-33-31-30-28-26-24-23-13-12-10-9-7-6-5-4-2\tM_m02553c\t665.124771868\t43-41-39-37-35-33-31-30-28-26-24-23-13-12-10-9-7-6-5-4-2\tR_HMR_4315\t1.007825032000028\t33,23,12,35,24,13,37,26,39,28,2,4,5,6,7,9,41,30,31,43,10\n+M_m01951c\t605.0771529799999\t37-35-33-31-29-27-26-24-14-13-11-9-7-6-4-2\tM_m01949c\t587.066588296\t37-35-33-31-29-27-26-24-14-13-11-9-7-6-4-2\tR_HMR_4399\t18.010564683999974\t33,11,35,24,13,14,37,26,27,29,2,4,6,7,9,31\n+M_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tM_m01285c\t427.02941494\t30-28-26-24-22-21-19-17-15-14\tR_HMR_8074\t79.96633052199996\t22,24,14,26,15,28,17,19,30,21\n+M_m00812s\t340.10056146\t16-2-3-22-20-18-5-7-8-10-12-15\tM_m01965s\t370.147511652\t25-22-20-18-16-15-24-12-10-8-7-5-3-2\tR_HMR_4832\t30.046950191999997\t22,12,15,16,18,2,3,5,7,8,20,10\n+M_m02845r\t230.01915394199997\t9-7-5-3-2\tM_m02846r\t230.019153942\t9-7-5-3-2\tR_HMR_4351\t2.8421709430404007E-14\t2,3,5,7,9\n+M_m02844c\t230.019153942\t13-11-9-8-6\tM_m02845c\t230.01915394199997\t9-8-11-13-6\tR_HMR_4354\t2.8421709430404007E-14\t11,13,6,8,9\n+M_m02845c\t230.01915394199997\t23-21-19-17-16\tM_m02884c\t290.04028331\t23-21-19-17-16-3-2\tR_HMR_4501\t60.02112936800003\t23,16,17,19,21\n+M_m03107c\t566.055020568\t35-33-31-29-27-25-24-22-12-11-9-6-4-3-2\tM_m01322c\t260.02971862600003\t31-29-27-25-24-22\tR_HMR_4131\t306.025301942\t22,24,25,27,29,31\n+M_m01169c\t276.024633246\t60-58-56-54-52-50\tM_m01596c\t43.98982924\t50\tR_HMR_4474\t232.034804006\t50\n+M_m03107g\t566.055020568\t24-22-58-56-54-52-51-49-12-11-9-6-4-3-2\tM_m03106g\t404.00219714799994\t24-22-12-11-9-6-4-3-2\tR_HMR_7674\t162.0528234200001\t22,11,12,24,2,3,4,6,9\n+M_m01746c\t260.029718626\t46-44-42-41-38-37\tM_m02955c\t339.99604914799994\t44-46-37-38-42-41\tR_HMR_4775\t79.96633052199996\t44,46,37,38,41,42\n+M_m02453c\t180.06338810399998\t42-40-38-36-34-33\tM_m02455c\t260.029718626\t33-34-42-40-38-36\tR_HMR_4490\t79.96633052199999\t33,34,36,38,40,42\n+M_m01961c\t258.01406856200003\t15-13-11-5-4-2\tM_m01169c\t276.024633246\t5-4-11-13-15-2\tR_HMR_4625\t18.010564683999974\t11,13,2,4,15,5\n+M_m01745c\t180.06338810399998\t42-40-38-37-34-33\tM_tag1p_D_c\t260.029718626\t37-38-40-42-34-33\tR_KHK3\t79.96633052199999\t33,34,37,38,40,42\n+M_m01746c\t260.029718626\t15-13-11-10-7-6\tM_m01690c\t169.99802457399997\t15-7-6\tR_HMR_8762\t90.031694052\t15,6,7\n+M_m01285c\t427.02941494\t30-28-26-24-22-21-19-17-15-14\tM_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tR_HMR_9800\t79.96633052199996\t22,24,14,26,15,28,17,19,30,21\n+M_m01159c\t164.06847348399998\t41-39-37-36-35-33\tM_m02372c\t244.034804006\t33-41-39-37-35-36\tR_HMR_4402\t79.96633052200002\t33,35,36,37,39,41\n+M_m01939c\t169.998024574\t8-6-4\tM_m00640c\t214.024239322\t8-6-4-3-2\tR_HMR_4398\t44.026214748\t4,6,8\n+M_m02845c\t230.01915394199997\t40-38-36-34-33\tM_m02806c\t389.951814986\t33-40-38-36-34\tR_HMR_4052\t159.932661044\t33,34,36,38,40\n+M_m01840c\t180.06338810399998\t55-53-46-47-49-51\tM_m01682c\t182.07903816799998\t55-53-51-49-47-46\tR_HMR_4315\t2.015650063999999\t55,46,47,49,51,53\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2CarbonSkeletonNet/test-data/Human-GEM_pathways.xml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,163 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CompoundGraph -i "$inputPath" +#if str($inputSide) != 'None': + -sc "$inputSide" +#end if +#if str($mergingStrat): + -mc "$mergingStrat" +#end if + $mergeEdges + $removeIsolated + $degree +#if str($weightFile) != 'None': + -cw "$weightFile" +#end if + $undirected + $computeWeight +#if str($format): + -f "$format" +#end if + -o "$output" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/> + <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (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="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/> + <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> + <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/> + <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> + <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/> + <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + <test> + + + + <param name="inputPath" value="XF_network.sbml"/> + + + + <param name="inputSide" value="XF_network_C_Side.tab"/> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + + <assert_contents> + + + + <has_line_matching expression=".*node.*" n="1101"/> + + + + <has_line_matching expression=".*edge.*" n="5581"/> + + + + </assert_contents> + + + + </output> + + + + </test> + <test> + + + + <param name="inputPath" value="XF_network.sbml"/> + + + + <param name="inputSide" value="XF_network_C_Side.tab"/> + + + + <param name="undirected" value="true"/> + + + + <param name="computeWeight" value="true"/> + + + + <param name="removeIsolated" value="true"/> + + + + <param name="degree" value="true"/> + + + + <param name="mergingStrat" value="by_id"/> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + + <assert_contents> + + + + <has_line_matching expression=".*node.*" n="793"/> + + + + <has_line_matching expression=".*edge.*" n="9372"/> + + + + </assert_contents> + + + + </output> + + + + </test> + </tests> + <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. +While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations. +In contrary to the Sbml2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2CompoundGraph/test-data/XF_network.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2CompoundGraph/test-data/XF_network.sbml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2CompoundGraph/test-data/XF_network_C_Side.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2CompoundGraph/test-data/XF_network_C_Side.tab Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2Graph/Sbml2Graph.xml --- a/tools/convert/Sbml2Graph/Sbml2Graph.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/convert/Sbml2Graph/Sbml2Graph.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,62 +1,172 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="develop"> <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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" $bipartite $compound $reaction - $tab - $gml - -o "$outputPath" +#if str($format): + -f "$format" +#end if + -o "$output" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/> <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/> <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="export in tabulated file" name="tab" truevalue="-tab" type="boolean" value="false"/> - <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="txt" name="outputPath"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="inputPath" value="toy_model.xml"/> - <output name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + <assert_contents> - <has_n_lines n="101"/> + + + + <has_line_matching expression=".*node.*" n="8"/> + + + + <has_line_matching expression=".*edge.*" n="9"/> + + + </assert_contents> + + + </output> + + + </test> <test> + + + <param name="inputPath" value="toy_model.xml"/> + + + <param name="bipartite" value="true"/> + + + <param name="compound" value="false"/> - <output name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + <assert_contents> - <has_n_lines n="184"/> + + + + <has_line_matching expression=".*node.*" n="15"/> + + + + <has_line_matching expression=".*edge.*" n="17"/> + + + </assert_contents> + + + </output> + + + </test> <test> + + + <param name="inputPath" value="toy_model.xml"/> + + + <param name="reaction" value="true"/> + + + <param name="compound" value="false"/> - <output name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output name="output"> + + + <assert_contents> - <has_n_lines n="90"/> + + + + + <has_line_matching expression=".*node.*" n="7"/> + + + + <has_line_matching expression=".*edge.*" n="8"/> + + + + </assert_contents> + + + + </output> + + + </test> </tests> <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format. -The graph can be either a compound graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> - <citations/> +The graph can be either a compound graph, a reaction graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> + <citations> + <citation type="doi">10.1109/tcbb.2008.79</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2PathwayNet/Sbml2PathwayNet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2PathwayNet/Sbml2PathwayNet.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,47 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Sbml2PathwayNet" name="Sbml2PathwayNet" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2PathwayNet -i "$inputPath" +#if str($inputSide) != 'None': + -sc "$inputSide" +#end if + $removeIsolated + $onlySourcesAndSinks +#if str($weightFile) != 'None': + -cw "$weightFile" +#end if + $connectors +#if str($format): + -f "$format" +#end if + -o "$outputPath" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-sc" format="txt" label="input Side compound file (recommended)" name="inputSide" optional="true" type="data" value=""/> + <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> + <param argument="-oss" checked="false" falsevalue="" label="consider only metabolites that are source or sink in the pathway (i.e non-intermediary compounds)" name="onlySourcesAndSinks" truevalue="-oss" type="boolean" value="false"/> + <param argument="-cw" format="tsv" label="an optional file containing weights for pathway pairs" name="weightFile" optional="true" type="data" value=""/> + <param argument="-ncw" checked="false" falsevalue="" label="set number of connecting compounds as weight" name="connectors" truevalue="-ncw" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> + </inputs> + <outputs> + <data format="txt" name="outputPath"/> + </outputs> + <tests/> + <help><![CDATA[Creation of a Pathway Network representation of a SBML file content +Genome-scale metabolic networks are often partitioned into metabolic pathways. Pathways are frequently considered independently despite frequent coupling in their activity due to shared metabolites. In order to decipher the interconnections linking overlapping pathways, this app proposes the creation of "Pathway Network", where two pathways are linked if they share compounds.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/Sbml2Tab/Sbml2Tab.xml --- a/tools/convert/Sbml2Tab/Sbml2Tab.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/convert/Sbml2Tab/Sbml2Tab.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,63 +1,305 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="MET4J_VERSION_TEST"> - <description>Create a tabulated file from a SBML file</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="develop"> + <description>Create a tabulated file listing reaction 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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): - -i "$i" + -irr "$i" #end if #if str($r): - -r "$r" + -rev "$r" #end if - -in "$in" - -out "$out" + -i "$in" + -o "$out" ]]></command> <inputs> - <param argument="-i" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> + <param argument="-irr" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> </sanitizer> </param> - <param argument="-r" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>"> + <param argument="-rev" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> </sanitizer> </param> - <param argument="-in" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/> + <param argument="-i" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/> </inputs> <outputs> <data format="tsv" name="out"/> </outputs> <tests> <test> + + + + + + + + + + + <param name="in" value="toy_model.xml"/> + + + + + + + + + + + <output ftype="tsv" name="out"> - <assert_contents> - <has_n_lines n="8"/> - <has_n_columns n="9"/> - <has_text text="2.0 E[c] --> D[c]"/> - <has_text text="A[c] <==> B[c]"/> - </assert_contents> - </output> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <has_n_lines n="8"/> + + + + + + + + + + + + <has_n_columns n="9"/> + + + + + + + + + + + + <has_text text="2.0 E[c] --> D[c]"/> + + + + + + + + + + + + <has_text text="A[c] <==> B[c]"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + </test> <test> + + + + + + + + + + + <param name="in" value="toy_model.xml"/> + + + + + + + + + + + <param name="i" value="->"/> + + + + + + + + + + + <param name="r" value="="/> + + + + + + + + + + + <output ftype="tsv" name="out"> - <assert_contents> - <has_n_lines n="8"/> - <has_n_columns n="9"/> - <has_text text="2.0 E[c] -> D[c]"/> - <has_text text="A[c] = B[c]"/> - </assert_contents> - </output> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <has_n_lines n="8"/> + + + + + + + + + + + + <has_n_columns n="9"/> + + + + + + + + + + + + <has_text text="2.0 E[c] -> D[c]"/> + + + + + + + + + + + + <has_text text="A[c] = B[c]"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> - <help><![CDATA[Create a tabulated file from a SBML file]]></help> + <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> <citations/> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/SbmlWizard/SbmlWizard.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/SbmlWizard/SbmlWizard.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,231 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SbmlWizard" name="SbmlWizard" version="develop"> + <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:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath" +#if str($inputSide) != 'None': + -rc "$inputSide" +#end if +#if str($toKeepC) != 'None': + -kc "$toKeepC" +#end if + $removeIsolated +#if str($inputReactions) != 'None': + -rr "$inputReactions" +#end if +#if str($toKeepR) != 'None': + -kr "$toKeepR" +#end if + $removeNoFlux +#if str($mergingStrat): + -mc "$mergingStrat" +#end if + $removeDuplicated +#if str($exchangeCompToRemove): + -rEX "$exchangeCompToRemove" +#end if + -o "$outputPath" +]]></command> + <inputs> + <param argument="-i" 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="-kc" format="txt" label="file containing identifiers of compounds to keep from the metabolic network" name="toKeepC" 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="-kr" format="txt" label="file containing identifiers of reactions to keep from the metabolic network" name="toKeepR" 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 1274e2a62479 -r 0976a6257300 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 Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 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 Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 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 Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 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 Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +R_ACGS +R_GLUN |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/convert/Tab2Sbml/Tab2Sbml.xml --- a/tools/convert/Tab2Sbml/Tab2Sbml.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/convert/Tab2Sbml/Tab2Sbml.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="MET4J_VERSION_TEST">\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="develop">\n <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != \'nan\':\n -ci "$colid"\n@@ -19,12 +19,12 @@\n -e "$e"\n #end if\n #if str($i):\n- -i "$i"\n+ -irr "$i"\n #end if\n #if str($r):\n- -r "$r"\n+ -rev "$r"\n #end if\n- -in "$in"\n+ -i "$in"\n #if str($id):\n -id "$id"\n #end if\n@@ -35,7 +35,7 @@\n #if str($nSkip) != \'nan\':\n -n "$nSkip"\n #end if\n- -sbml "$sbml"\n+ -o "$sbml"\n ]]></command>\n <inputs>\n <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/>\n@@ -47,17 +47,17 @@\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n- <param argument="-i" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->">\n+ <param argument="-irr" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n- <param argument="-r" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>">\n+ <param argument="-rev" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n- <param argument="-in" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/>\n+ <param argument="-i" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/>\n <param argument="-id" label="[NA] Model id written in the SBML file" name="id" optional="true" type="text" value="NA">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n@@ -76,63 +76,657 @@\n </outputs>\n <tests>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="in" value="toy_model.tsv"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="sbml" name="sbml">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <is_valid_xml/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*reaction .*" n="7"/>\n+ \n+ \n+ \n'..b' \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <is_valid_xml/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*id=.R_reac2.*" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="in" value="toy_model.tsv"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="id" value="myModel"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="sbml" name="sbml">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <is_valid_xml/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression=".*myModel.*" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/mapping/NameMatcher/NameMatcher.xml --- a/tools/mapping/NameMatcher/NameMatcher.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/mapping/NameMatcher/NameMatcher.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_NameMatcher" name="NameMatcher" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_NameMatcher" name="NameMatcher" version="develop"> <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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.NameMatcher#if str($n): -nMatch "$n" @@ -16,7 +16,7 @@ #if str($col): -col "$col" #end if - -sbml "$sbml" + -i "$sbml" -compound "$input" #if str($comment): -c "$comment" @@ -27,7 +27,7 @@ -o "$outputFile" ]]></command> <inputs> - <param argument="-nMatch" label="[1] Number of match to return per name" name="n" optional="true" type="text" value="1"> + <param argument="-nMatch" label="[1] Number of matchs to return per name" name="n" optional="true" type="text" value="1"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> </sanitizer> @@ -42,7 +42,7 @@ <valid initial="string.printable"/> </sanitizer> </param> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> + <param argument="-i" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> <param argument="-compound" format="tsv" label="Compound file containing one column with compound names to search among the SBML entries" name="input" optional="false" type="data" value=""/> <param argument="-c" label="[#] Comment String in the compound file. The lines beginning by this string won't be read" name="comment" optional="true" type="text" value="#"> <sanitizer invalid_char="_"> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml --- a/tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,12 +1,286 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="MET4J_VERSION_TEST">\n- <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.\n-The fisher exact test compute the probability p to randomly get the given set of value. \n-This version compute the probability to get at least the given overlap between the given set and the given modality :\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="develop">\n+ <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.</description>\n+ <xrefs>\n+ <xref type="bio.tools">met4j</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != \'nan\':\n+ -th "$th"\n+#end if\n+ -i "$sbml"\n+ -d "$input"\n+#if str($corr):\n+ -c "$corr"\n+#end if\n+ -o "$outputFile"\n+]]></command>\n+ <inputs>\n+ <param argument="-th" label="threshold to select significant pathways. No filtering if <=0" name="th" optional="true" type="float" value="0.0"/>\n+ <param argument="-i" format="sbml" label="Input model : SBML file with pathway annotation" name="sbml" optional="false" type="data" value=""/>\n+ <param argument="-d" format="tsv" label="Input data : Compounds of interest file, as one SBML specie identifier per line" name="input" optional="false" type="data" value=""/>\n+ <param argument="-c" label="Method for multiple testing p-value adjustment." name="corr" optional="true" type="select" value="BenjaminiHochberg">\n+ <option value="Bonferroni">Bonferroni</option>\n+ <option selected="true" value="BenjaminiHochberg">BenjaminiHochberg</option>\n+ <option value="HolmBonferroni">HolmBonferroni</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data format="tsv" name="outputFile"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <param name="sbml" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <param name="input" value="XF_network_C_NOI.txt"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <output name="outputFile">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <has_n_columns n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <has_n_lines n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </output>\n+'..b'+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ <has_n_lines n="2"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ </test>\n+ </tests>\n+ <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.\n+The fisher exact test computes the probability p to randomly get the given set of values. \n+This version computes the probability to get at least the given overlap between the given set and the given modality :\n Sum the hypergeometric probability with increasing target/query intersection cardinality.\n \n The hypergeometric probability is computed from the following contingency table entries.\n-(value in cells correspond to the marginal totals of each intersection groups)\n+(values in cells correspond to the marginal totals of each intersection groups)\n \t\t\t\tQuery\t!Query\n \tTarget\t\ta\t\tb\n \t!Target\t\tc\t\td\n@@ -18,60 +292,6 @@\n - Bonferroni: adjusted p-value = p*n\n - Benjamini-Hochberg: adjusted p-value = p*n/k\n - Holm-Bonferroni: adjusted p-value = p*(n+1-k)\n-n : number of tests; k : pvalue rank</description>\n- <xrefs>\n- <xref type="bio.tools">met4j</xref>\n- </xrefs>\n- <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>\n- </requirements>\n- <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != \'nan\':\n- -th "$th"\n-#end if\n- -s "$sbml"\n- -i "$input"\n-#if str($corr):\n- -c "$corr"\n-#end if\n- -o "$outputFile"\n-]]></command>\n- <inputs>\n- <param argument="-th" label="threshold to select significant pathways. No filtering if <=0" name="th" optional="true" type="float" value="0.0"/>\n- <param argument="-s" format="sbml" label="Input model : SBML file with pathway annotation" name="sbml" optional="false" type="data" value=""/>\n- <param argument="-i" format="tsv" label="Input data : Compounds of interest file, as one SBML specie identifier per line" name="input" optional="false" type="data" value=""/>\n- <param argument="-c" label="Method for multiple testing p-value adjustment." name="corr" optional="true" type="select" value="BenjaminiHochberg">\n- <option value="Bonferroni">Bonferroni</option>\n- <option selected="true" value="BenjaminiHochberg">BenjaminiHochberg</option>\n- <option value="HolmBonferroni">HolmBonferroni</option>\n- </param>\n- </inputs>\n- <outputs>\n- <data format="tsv" name="outputFile"/>\n- </outputs>\n- <tests>\n- <test>\n- <param name="sbml" value="XF_network.sbml"/>\n- <param name="input" value="XF_network_C_NOI.txt"/>\n- <output name="outputFile">\n- <assert_contents>\n- <has_n_columns n="3"/>\n- <has_n_lines n="3"/>\n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="sbml" value="XF_network.sbml"/>\n- <param name="input" value="XF_network_C_NOI.txt"/>\n- <param name="corr" value="HolmBonferroni"/>\n- <param name="th" value="0.005"/>\n- <output name="outputFile">\n- <assert_contents>\n- <has_n_columns n="3"/>\n- <has_n_lines n="2"/>\n- </assert_contents>\n- </output>\n- </test>\n- </tests>\n- <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.]]></help>\n+n : number of tests; k : pvalue rank]]></help>\n <citations/>\n </tool>\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/met4j.yml --- a/tools/met4j.yml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/met4j.yml Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -3,49 +3,49 @@ install_resolver_dependencies: true install_tool_dependencies: false tools: - - name: DecomposeSBML + - name: ExtractAnnotations owner: metexplore tool_panel_section_id: met4j_attributes - name: ExtractPathways owner: metexplore tool_panel_section_id: met4j_attributes - - name: ExtractSbmlAnnot + - name: GetEntities owner: metexplore tool_panel_section_id: met4j_attributes - name: GetGenesFromReactions owner: metexplore tool_panel_section_id: met4j_attributes + - name: GetMetaboliteAttributes + owner: metexplore + tool_panel_section_id: met4j_attributes - name: GetReactantsFromReactions owner: metexplore tool_panel_section_id: met4j_attributes - - name: SbmlSetChargesFromFile + - name: SetCharges owner: metexplore tool_panel_section_id: met4j_attributes - - name: SbmlSetEcsFromFile + - name: SetChemicalFormulas owner: metexplore tool_panel_section_id: met4j_attributes - - name: SbmlSetFormulasFromFile + - name: SetEcNumbers owner: metexplore tool_panel_section_id: met4j_attributes - - name: SbmlSetGprsFromFile + - name: SetGprs owner: metexplore tool_panel_section_id: met4j_attributes - - name: SbmlSetIdsFromFile + - name: SetIds owner: metexplore tool_panel_section_id: met4j_attributes - - name: SbmlSetNamesFromFile + - name: SetNames owner: metexplore tool_panel_section_id: met4j_attributes - - name: SbmlSetPathwaysFromFile + - name: SetPathways owner: metexplore tool_panel_section_id: met4j_attributes - - name: SbmlSetRefsFromFile + - name: SetReferences owner: metexplore tool_panel_section_id: met4j_attributes - - name: SbmlToMetaboliteTable - owner: metexplore - tool_panel_section_id: met4j_attributes - - name: GetModelProteome + - name: GetBiggModelProteome owner: metexplore tool_panel_section_id: met4j_bigg - name: FbcToNotes @@ -54,15 +54,24 @@ - name: Kegg2Sbml owner: metexplore tool_panel_section_id: met4j_convert - - name: SBMLwizard + - name: Sbml2CarbonSkeletonNet + owner: metexplore + tool_panel_section_id: met4j_convert + - name: Sbml2CompoundGraph owner: metexplore tool_panel_section_id: met4j_convert - name: Sbml2Graph owner: metexplore tool_panel_section_id: met4j_convert + - name: Sbml2PathwayNet + owner: metexplore + tool_panel_section_id: met4j_convert - name: Sbml2Tab owner: metexplore tool_panel_section_id: met4j_convert + - name: SbmlWizard + owner: metexplore + tool_panel_section_id: met4j_convert - name: Tab2Sbml owner: metexplore tool_panel_section_id: met4j_convert @@ -75,18 +84,12 @@ - name: BipartiteDistanceMatrix owner: metexplore tool_panel_section_id: met4j_networkanalysis - - name: CarbonSkeletonNet - owner: metexplore - tool_panel_section_id: met4j_networkanalysis - name: ChemSimilarityWeighting owner: metexplore tool_panel_section_id: met4j_networkanalysis - name: ChokePoint owner: metexplore tool_panel_section_id: met4j_networkanalysis - - name: CompoundNet - owner: metexplore - tool_panel_section_id: met4j_networkanalysis - name: DegreeWeighting owner: metexplore tool_panel_section_id: met4j_networkanalysis @@ -111,9 +114,6 @@ - name: NetworkSummary owner: metexplore tool_panel_section_id: met4j_networkanalysis - - name: PathwayNet - owner: metexplore - tool_panel_section_id: met4j_networkanalysis - name: PrecursorNetwork owner: metexplore tool_panel_section_id: met4j_networkanalysis @@ -132,6 +132,9 @@ - name: TopologicalPathwayAnalysis owner: metexplore tool_panel_section_id: met4j_networkanalysis + - name: CreateMetaNetwork + owner: metexplore + tool_panel_section_id: met4j_reconstruction - name: SbmlCheckBalance owner: metexplore tool_panel_section_id: met4j_reconstruction |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml --- a/tools/networkAnalysis/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="develop"> <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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.BipartiteDistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -42,7 +42,7 @@ </outputs> <tests/> <help><![CDATA[Create a compound to reactions distance matrix. -The distance between two nodes (metabolite or reaction) is computed as the length of the shortest path connecting the two in the bipartite graph, Bipartite graph are composed of two distinct sets of nodes and two nodes can be linked only if they are from distinct sets. +The distance between two nodes (metabolite or reaction) is computed as the length of the shortest path connecting the two in the bipartite graph, Bipartite graphs are composed of two distinct sets of nodes and two nodes can be linked only if they are from distinct sets. Therefore a metabolite node can be linked to a reaction node if the metabolite is a substrate or product of the reaction. An optional custom edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path.Custom weighting can be provided in a file. In that case, edges without weight are ignored during path search. If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml --- a/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,122 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath" - -g "$inputAAM" - $keepSingleCarbon - $mergeComp - $mergeEdges - $removeIsolated - $undirected - $computeWeight - $asMatrix - $main - $fromIndexes - -o "$outputPath" -]]></command> - <inputs> - <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-g" format="gsam" label="input GSAM file" name="inputAAM" optional="false" type="data" value=""/> - <param argument="-ks" checked="false" falsevalue="" label="keep edges involving single-carbon compounds, such as CO2 (requires formulas in SBML)" name="keepSingleCarbon" truevalue="-ks" type="boolean" value="false"/> - <param argument="-mc" checked="false" falsevalue="" label="merge compartments (requires unique compound names that are consistent across compartments)" name="mergeComp" truevalue="-mc" type="boolean" value="false"/> - <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/> - <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> - <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/> - <param argument="-tp" checked="false" falsevalue="" label="set transition probability as weight" name="computeWeight" truevalue="-tp" type="boolean" value="false"/> - <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/> - <param argument="-main" checked="false" falsevalue="" label="Compute RPAIRS-like tags and keep only main transitions for each reaction" name="main" truevalue="-main" type="boolean" value="false"/> - <param argument="-i" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-i" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="gml" name="outputPath"/> - </outputs> - <tests> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2602"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="keepSingleCarbon" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2629"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="mergeComp" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2406"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="mergeEdges" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2071"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="removeIsolated" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2490"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="undirected" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="3214"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> - <param name="asMatrix" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="112"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="Human-GEM_pathways.xml"/> - <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/> - <param name="fromIndexes" value="true"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines n="2611"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produce a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) perform atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab --- a/tools/networkAnalysis/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,205 +0,0 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|
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab --- a/tools/networkAnalysis/CarbonSkeletonNet/test-data/Human-GEM_pathways-transitions2.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,206 +0,0 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. 23-21-19-17-16\tM_m01761c\t230.019153942\t23-21-19-17-16 . 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t260.029718626\t46-44-42-41-38-37\tM_m02955c\t339.99604914799994\t44-46-37-38-42-41\tR_HMR_4775\t79.96633052199996\t44,46,37,38,41,42\n-M_m02453c\t180.06338810399998\t42-40-38-36-34-33\tM_m02455c\t260.029718626\t33-34-42-40-38-36\tR_HMR_4490\t79.96633052199999\t33,34,36,38,40,42\n-M_m01961c\t258.01406856200003\t15-13-11-5-4-2\tM_m01169c\t276.024633246\t5-4-11-13-15-2\tR_HMR_4625\t18.010564683999974\t11,13,2,4,15,5\n-M_m01745c\t180.06338810399998\t42-40-38-37-34-33\tM_tag1p_D_c\t260.029718626\t37-38-40-42-34-33\tR_KHK3\t79.96633052199999\t33,34,37,38,40,42\n-M_m01746c\t260.029718626\t15-13-11-10-7-6\tM_m01690c\t169.99802457399997\t15-7-6\tR_HMR_8762\t90.031694052\t15,6,7\n-M_m01285c\t427.02941494\t30-28-26-24-22-21-19-17-15-14\tM_m01371c\t506.99574546199995\t30-28-26-24-22-21-19-17-15-14\tR_HMR_9800\t79.96633052199996\t22,24,14,26,15,28,17,19,30,21\n-M_m01159c\t164.06847348399998\t41-39-37-36-35-33\tM_m02372c\t244.034804006\t33-41-39-37-35-36\tR_HMR_4402\t79.96633052200002\t33,35,36,37,39,41\n-M_m01939c\t169.998024574\t8-6-4\tM_m00640c\t214.024239322\t8-6-4-3-2\tR_HMR_4398\t44.026214748\t4,6,8\n-M_m02845c\t230.01915394199997\t40-38-36-34-33\tM_m02806c\t389.951814986\t33-40-38-36-34\tR_HMR_4052\t159.932661044\t33,34,36,38,40\n-M_m01840c\t180.06338810399998\t55-53-46-47-49-51\tM_m01682c\t182.07903816799998\t55-53-51-49-47-46\tR_HMR_4315\t2.015650063999999\t55,46,47,49,51,53\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/CarbonSkeletonNet/test-data/Human-GEM_pathways.xml --- a/tools/networkAnalysis/CarbonSkeletonNet/test-data/Human-GEM_pathways.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,7661 +0,0 @@\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 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml --- a/tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="develop"> <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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type): -f "$type" @@ -65,6 +65,10 @@ <data format="tsv" name="outputPath"/> </outputs> <tests/> - <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search. See McSha et al. 2003 (https://doi.org/10.1093/bioinformatics/btg217), Rahman et al. 2005 (https://doi.org/10.1093/bioinformatics/bti116) and Pertusi et al. 2014 (https://doi.org/10.1093/bioinformatics/btu760)]]></help> - <citations/> + <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search.]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btg217</citation> + <citation type="doi">10.1093/bioinformatics/bti116</citation> + <citation type="doi">10.1093/bioinformatics/btu760</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/ChokePoint/ChokePoint.xml --- a/tools/networkAnalysis/ChokePoint/ChokePoint.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/ChokePoint/ChokePoint.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ChokePoint" name="ChokePoint" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ChokePoint" name="ChokePoint" version="develop"> <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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath" -o "$outputPath" @@ -18,19 +18,130 @@ </outputs> <tests> <test> - <param name="inputPath" value="XF_network.sbml"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <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_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --> M_ac_c \+ M_gam6p_c" n="1"/> - </assert_contents> - </output> - </test> + + + + + + + + + + + + <param name="inputPath" value="XF_network.sbml"/> + + + + + + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <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_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. -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/> +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.]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btl181</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/CompoundNet/CompoundNet.xml --- a/tools/networkAnalysis/CompoundNet/CompoundNet.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,78 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_CompoundNet" name="CompoundNet" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath" -#if str($inputSide) != 'None': - -sc "$inputSide" -#end if -#if str($mergingStrat): - -mc "$mergingStrat" -#end if - $mergeEdges - $removeIsolated - $degree -#if str($weightFile) != 'None': - -cw "$weightFile" -#end if - $undirected - $computeWeight - $asMatrix - -o "$outputPath" -]]></command> - <inputs> - <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/> - <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (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="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/> - <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> - <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/> - <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> - <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/> - <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/> - <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="gml" name="outputPath"/> - </outputs> - <tests> - <test> - <param name="inputPath" value="XF_network.sbml"/> - <param name="inputSide" value="XF_network_C_Side.tab"/> - <output name="outputPath"> - <assert_contents> - <has_line_matching expression=".*node.*" n="1101"/> - <has_line_matching expression=".*edge.*" n="5581"/> - </assert_contents> - </output> - </test> - <test> - <param name="inputPath" value="XF_network.sbml"/> - <param name="inputSide" value="XF_network_C_Side.tab"/> - <param name="undirected" value="true"/> - <param name="computeWeight" value="true"/> - <param name="removeIsolated" value="true"/> - <param name="degree" value="true"/> - <param name="mergingStrat" value="by_id"/> - <output name="outputPath"> - <assert_contents> - <has_line_matching expression=".*node.*" n="793"/> - <has_line_matching expression=".*edge.*" n="9372"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. -While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations. -In contrary to the SBML2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree² weighting to get relevant structure without structural data.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help> - <citations/> -</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/CompoundNet/test-data/XF_network.sbml --- a/tools/networkAnalysis/CompoundNet/test-data/XF_network.sbml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47267 +0,0 @@\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 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/CompoundNet/test-data/XF_network_C_Side.tab --- a/tools/networkAnalysis/CompoundNet/test-data/XF_network_C_Side.tab Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -M_atp_c -M_h2o_c -M_pi_c -M_adp_c -M_ppi_c -M_h_c |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml --- a/tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="develop"> <description>Provides tabulated compound graph edge list, with one column with target's degree.</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> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DegreeWeighting#if str($pow): -pow "$pow" @@ -45,6 +45,8 @@ <data format="tsv" name="outputPath"/> </outputs> <tests/> - <help><![CDATA[Provides tabulated compound graph edge list, with one column with target's degree.Degree has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search. See Croes et al. 2006 (https://doi.org/10.1016/j.jmb.2005.09.079) and Croes et al. 2005 (https://doi.org/10.1093/nar/gki437)]]></help> - <citations/> + <help><![CDATA[Provides tabulated compound graph edge list, with one column with target's degree.Degree has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search.]]></help> + <citations> + <citation type="doi">10.1016/j.jmb.2005.09.079</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml --- a/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="develop"> <description>Create a compound to compound distance matrix.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -34,30 +34,294 @@ </outputs> <tests> <test> + + + + + + + + + + + <param name="inputPath" value="toy_model.xml"/> + + + + + + + + + + + <output ftype="csv" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <has_n_lines n="9"/> + + + + + + + + + + + <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/> + + + + + + + + + + + <has_line_matching expression="B,1.0,Infinity,0.0,2.0,1.0,2.0,Infinity,Infinity" n="1"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> <test> + + + + + + + + + + + <param name="inputPath" value="toy_model.xml"/> + + + + + + + + + + + <param name="sideCompoundFile" value="sides.txt"/> + + + + + + + + + + + <param name="degree" value="true"/> + + + + + + + + + + + <param name="undirected" value="true"/> + + + + + + + + + + + <output ftype="csv" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <has_n_lines n="8"/> + + + + + + + + + + + <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/> + + + + + + + + + + + <has_line_matching expression="A,0.0,4.0,4.0,20.0,21.0,24.0,25.0" n="1"/> + + + + + + + + + + + <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/> + + + + + + + + + + + <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/> + + + + + + + + + + + <has_line_matching expression="D,8.0,4.0,4.0,0.0,1.0,4.0,5.0" n="1"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> <help><![CDATA[Create a compound to compound distance matrix. |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml --- a/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,17 +1,16 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="MET4J_VERSION_TEST"> - <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="develop"> + <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</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> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath" -s "$sourcePath" -t "$targetPath" $undirected - $asTable -sc "$sideCompoundFile" #if str($blkdReactionFile) != 'None': -br "$blkdReactionFile" @@ -23,14 +22,16 @@ -k "$k" #end if $st - -o "$outputPath" +#if str($format): + -f "$format" +#end if + -o "$output" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/> <param argument="-br" format="txt" label="a file containing list of blocked reactions to ignore" name="blkdReactionFile" optional="true" type="data" value=""/> <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/> @@ -40,26 +41,70 @@ </sanitizer> </param> <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="outputPath"/> + <data format="txt" name="output"/> </outputs> <tests> <test> - <param name="inputPath" value="toy_model.xml"/> - <param name="sourcePath" value="seeds.txt"/> - <param name="targetPath" value="targets.txt"/> - <param name="sideCompoundFile" value="sc.txt"/> - <output ftype="gml" name="outputPath"> - <assert_contents> - <has_line_matching expression=".*node.*" n="5"/> - <has_line_matching expression=".*edge.*" n="4"/> - </assert_contents> - </output> - </test> + + + + <param name="inputPath" value="toy_model.xml"/> + + + + <param name="sourcePath" value="seeds.txt"/> + + + + <param name="targetPath" value="targets.txt"/> + + + + <param name="sideCompoundFile" value="sc.txt"/> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + + <assert_contents> + + + + <has_line_matching expression=".*node.*" n="5"/> + + + + <has_line_matching expression=".*edge.*" n="4"/> + + + + </assert_contents> + + + + </output> + + + + </test> </tests> - <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. -The subnetwork corresponds to part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list. + <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. +The subnetwork corresponds to the part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list. Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.]]></help> <citations/> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml --- a/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="MET4J_VERSION_TEST"> - <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="develop"> + <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath" -s "$sourcePath" @@ -19,12 +19,14 @@ #end if $chemicalSim $undirected - $asTable #if str($k): -k "$k" #end if $st - -o "$outputPath" +#if str($format): + -f "$format" +#end if + -o "$output" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> @@ -35,41 +37,82 @@ <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> <param argument="-sw" checked="false" falsevalue="" label="penalize traversal of non-relevant edges by using chemical similarity weighting" name="chemicalSim" truevalue="-sw" type="boolean" value="false"/> <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> </sanitizer> </param> <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="outputPath"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="inputPath" value="toy_model.xml"/> + + + <param name="sourcePath" value="seeds.txt"/> + + + <param name="targetPath" value="targets.txt"/> - <output ftype="gml" name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + <assert_contents> + + + <has_line_matching expression=".*node.*" n="3"/> + + + <has_line_matching expression=".*edge.*" n="2"/> + + + </assert_contents> + + + </output> + + + </test> </tests> - <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row. -The subnetwork correspond to part of the network that connects compounds from the first list to compounds from the second list. + <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row. +The subnetwork corresponds to the part of the network that connects compounds from the first list to compounds from the second list. Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting. -See previous works on subnetwork extraction for parameters recommendations:Frainay, C., & Jourdan, F. Computational methods to identify metabolic sub-networks based on metabolomic profiles. Bioinformatics 2016;1–14. https://doi.org/10.1093/bib/bbv115 -Faust, K., Croes, D., & van Helden, J. Prediction of metabolic pathways from genome-scale metabolic networks. Bio Systems 2011;105(2), 109–121. https://doi.org/10.1016/j.biosystems.2011.05.004 -Croes D, Couche F, Wodak SJ, et al. Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res 2005;33:W326–30. -Croes D, Couche F, Wodak SJ, et al. Inferring meaningful pathways in weighted metabolic networks. J Mol Biol 2006; 356:222–36. -Rahman SA, Advani P, Schunk R, et al. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics 2005;21:1189–93. -Pertusi DA, Stine AE, Broadbelt LJ, et al. Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics 2014;1–9. -McShan DC, Rao S, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics 2003;19:1692–8. -]]></help> - <citations/> +See previous works on subnetwork extraction for parameters recommendations.]]></help> + <citations> + <citation type="doi">10.1093/bib/bbv115</citation> + <citation type="doi">10.1016/j.biosystems.2011.05.004</citation> + <citation type="doi">10.1016/j.jmb.2005.09.079</citation> + <citation type="doi">10.1093/bioinformatics/btu760</citation> + <citation type="doi">10.1093/nar/gki437</citation> + <citation type="doi">10.1093/bioinformatics/bti116</citation> + <citation type="doi">10.1093/bioinformatics/btg217</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml --- a/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,16 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="MET4J_VERSION_TEST"> - <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="develop"> + <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</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> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath" -s "$sourcePath" $undirected - $asTable -t "$targetPath" -sc "$sideCompoundFile" #if str($rExclude) != 'None': @@ -23,13 +22,15 @@ -k "$k" #end if $st - -o "$outputPath" +#if str($format): + -f "$format" +#end if + -o "$output" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/> <param argument="-re" format="txt" label="an optional file containing list of reactions to ignore" name="rExclude" optional="true" type="data" value=""/> @@ -40,26 +41,70 @@ </sanitizer> </param> <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="outputPath"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="inputPath" value="toy_model.xml"/> + + + <param name="sourcePath" value="seeds.txt"/> + + + <param name="targetPath" value="targets.txt"/> + + + <param name="sideCompoundFile" value="sides.txt"/> - <output ftype="gml" name="outputPath"> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + <assert_contents> + + + <has_line_matching expression=".*node.*" n="3"/> + + + <has_line_matching expression=".*edge.*" n="2"/> + + + </assert_contents> + + + </output> + + + </test> </tests> - <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. -The subnetwork corresponds to part of the network that connects reactions from the first list to reactions from the second list. + <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. +The subnetwork corresponds to the part of the network that connects reactions from the first list to reactions from the second list. Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, reaction graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds to ignore for linking reactions must be provided. An optional edge weight file, if available, can also be used.]]></help> <citations/> </tool> |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/ExtractSubReactionNetwork/test-data/sides.txt --- a/tools/networkAnalysis/ExtractSubReactionNetwork/test-data/sides.txt Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/ExtractSubReactionNetwork/test-data/sides.txt Fri Jan 31 18:28:53 2025 +0000 |
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| @@ -0,0 +1,14 @@ +// Copyright 2025 lcottret +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// https://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/LoadPoint/LoadPoint.xml --- a/tools/networkAnalysis/LoadPoint/LoadPoint.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/LoadPoint/LoadPoint.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_LoadPoint" name="LoadPoint" version="MET4J_VERSION_TEST"> - <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug target.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_LoadPoint" name="LoadPoint" version="develop"> + <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</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> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -30,16 +30,104 @@ </outputs> <tests> <test> + + + + + + + + + + + <param name="inputPath" value="toy_model.xml"/> + + + + + + + + + + + <output ftype="tsv" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <has_n_columns n="3"/> + + + + + + + + + + + <has_n_lines n="8"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> - <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug target. + <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. From Rahman et al. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinf. (2006): For a given metabolic network, the load L on metabolite m can be defined as : ln [(pm/km)/(∑Mi=1Pi)/(∑Mi=1Ki)] @@ -48,5 +136,7 @@ P is the total number of shortest paths; K is the sum of links in the metabolic network of M metabolites (where M is the number of metabolites in the network). Use of the logarithm makes the relevant values more distinguishable.]]></help> - <citations/> + <citations> + <citation type="doi">10.1093/bioinformatics/btl181</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/MetaboRank/MetaboRank.xml --- a/tools/networkAnalysis/MetaboRank/MetaboRank.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/MetaboRank/MetaboRank.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_MetaboRank" name="MetaboRank" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_MetaboRank" name="MetaboRank" version="develop"> <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath" -s "$seedsFilePath" @@ -44,15 +44,125 @@ </outputs> <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> + + + + + + + + + + + + <has_n_lines n="1100"/> + + + + + + + + + + + + <has_n_columns n="11"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> </tests> <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network. @@ -60,6 +170,8 @@ The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining. It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks. For convenience, a one dimensional centrality rank is also computed from the highest rank from PageRank or CheiRank, and using lowest rank as tie-breaker. -See publication for more information: Frainay et al. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results, Bioinformatics (35-2), https://doi.org/10.1093/bioinformatics/bty577]]></help> - <citations/> +See publication for more information.]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/bty577</citation> + </citations> </tool> |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/NetworkSummary/NetworkSummary.xml --- a/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_NetworkSummary" name="NetworkSummary" version="MET4J_VERSION_TEST"> - <description>Create a report summarizing several graph measures characterising the structure of the network.</description> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_NetworkSummary" name="NetworkSummary" version="develop"> + <description>Create a report summarizing several graph measures characterising the structure 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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -26,14 +26,92 @@ </outputs> <tests> <test> - <param name="inputPath" value="toy_model.xml"/> - <output name="outputPath"> - <assert_contents> - <has_n_lines min="1"/> - </assert_contents> - </output> - </test> + + + + + + + + + + + + <param name="inputPath" value="toy_model.xml"/> + + + + + + + + + + + + <output name="outputPath"> + + + + + + + + + + + + <assert_contents> + + + + + + + + + + + + <has_n_lines min="1"/> + + + + + + + + + + + + </assert_contents> + + + + + + + + + + + + </output> + + + + + + + + + + + + </test> </tests> - <help><![CDATA[Use a metabolic network in SBML file and an optional list of side compounds, and produce a report summarizing several graph measures characterising the structure of the network.This includes (non-exhaustive list): size and order, connectivity, density, degree distribution, shortest paths length, top centrality nodes...]]></help> + <help><![CDATA[Create a report summarizing several graph measures characterising the structure of a metabolic network. +Use a metabolic network in SBML file and an optional list of side compounds, and produce a report summarizing several graph measures characterising the structure of the network.This includes (non-exhaustive list): size and order, connectivity, density, degree distribution, shortest paths length, top centrality nodes...]]></help> <citations/> </tool> |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/PathwayNet/PathwayNet.xml --- a/tools/networkAnalysis/PathwayNet/PathwayNet.xml Wed Jul 26 15:33:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,38 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_PathwayNet" name="PathwayNet" version="MET4J_VERSION_TEST"> - <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:MET4J_VERSION_TEST</container> - </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PathwayNet -s "$inputPath" -#if str($inputSide) != 'None': - -sc "$inputSide" -#end if - $removeIsolated - $onlySourcesAndSinks -#if str($weightFile) != 'None': - -cw "$weightFile" -#end if - $connectors - $asMatrix - -o "$outputPath" -]]></command> - <inputs> - <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-sc" format="txt" label="input Side compound file (recommended)" name="inputSide" optional="true" type="data" value=""/> - <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> - <param argument="-oss" checked="false" falsevalue="" label="consider only metabolites that are source or sink in the pathway (i.e non-intermediary compounds)" name="onlySourcesAndSinks" truevalue="-oss" type="boolean" value="false"/> - <param argument="-cw" format="tsv" label="an optional file containing weights for pathway pairs" name="weightFile" optional="true" type="data" value=""/> - <param argument="-ncw" checked="false" falsevalue="" label="set number of connecting compounds as weight" name="connectors" truevalue="-ncw" type="boolean" value="false"/> - <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/> - </inputs> - <outputs> - <data format="gml" name="outputPath"/> - </outputs> - <tests/> - <help><![CDATA[Genome-scale metabolic networks are often partitioned into metabolic pathways. Pathways are frequently considered independently despite frequent coupling in their activity due to shared metabolites. In order to decipher the interconnections linking overlapping pathways, this app proposes the creation of "Pathway Network", where two pathways are linked if they share compounds.]]></help> - <citations/> -</tool> |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml --- a/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="develop"> <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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" -t "$targetsFilePath" @@ -15,7 +15,9 @@ #if str($reactionToIgnoreFile) != 'None': -ir "$reactionToIgnoreFile" #end if - $asTable +#if str($format): + -f "$format" +#end if -o "$output" ]]></command> <inputs> @@ -23,21 +25,58 @@ <param argument="-t" format="txt" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/> <param argument="-sc" format="txt" label="an optional file containing list of ubiquitous compounds to be considered already available" name="sideCompoundFile" optional="true" type="data" value=""/> <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope)" name="reactionToIgnoreFile" optional="true" type="data" value=""/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="output"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="sbmlFilePath" value="toy_model.xml"/> + + + <param name="targetsFilePath" value="targets.txt"/> - <output ftype="gml" name="output"> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + <assert_contents> + + + <has_line_matching expression=".*node.*" n="13"/> + + + <has_line_matching expression=".*edge.*" n="15"/> + + + </assert_contents> + + + </output> + + + </test> </tests> <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml --- a/tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="MET4J_VERSION_TEST">\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="develop">\n <description>Create a reaction to reaction distance matrix.</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath"\n #if str($sideCompoundFile) != \'None\':\n@@ -38,91 +38,982 @@\n </outputs>\n <tests>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputPath" value="toy_model.xml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="csv" name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="8"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputPath" value="toy_model.xml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="undirected" value="true"/>\n+ \n+ \n+ \n+ \n+ \n'..b'\n+ \n+ \n </test>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputPath" value="toy_model.xml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="sideCompoundFile" value="sides.txt"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="rExclude" value="rexclude.txt"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output ftype="csv" name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="6"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n <help><![CDATA[Create a reaction to reaction distance matrix.\n' |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml --- a/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="develop"> <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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath" -s "$seedsFilePath" @@ -17,7 +17,9 @@ -ir "$reactionToIgnoreFile" #end if $trace - $asTable +#if str($format): + -f "$format" +#end if -o "$output" ]]></command> <inputs> @@ -27,26 +29,67 @@ <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/> <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope" name="reactionToIgnoreFile" optional="true" type="data" value=""/> <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" type="boolean" value="false"/> - <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> + <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id 	 edge type 	 target id). Other options include GML, JsonGraph, and tabulated node list (label 	 node id 	 node type)." name="format" optional="true" type="select" value="tab"> + <option value="gml">gml</option> + <option selected="true" value="tab">tab</option> + <option value="nodeList">nodeList</option> + <option value="json">json</option> + <option value="matrix">matrix</option> + </param> </inputs> <outputs> - <data format="gml" name="output"/> + <data format="txt" name="output"/> </outputs> <tests> <test> + + + <param name="sbmlFilePath" value="toy_model.xml"/> + + + <param name="seedsFilePath" value="seeds.txt"/> + + + <param name="sideCompoundFile" value="sides.txt"/> - <output ftype="gml" name="output"> + + + + <param name="format" value="gml"/> + + + + <output ftype="txt" name="output"> + + + <assert_contents> + + + <has_line_matching expression=".*node.*" n="9"/> + + + <has_line_matching expression=".*edge.*" n="11"/> + + + </assert_contents> + + + </output> + + + </test> </tests> <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network -The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction -For more information, see Handorf, Ebenhöh and Heinrich (2005). *Expanding metabolic networks: scopes of compounds, robustness, and evolution.* Journal of molecular evolution, 61(4), 498-512. (https://doi.org/10.1007/s00239-005-0027-1)]]></help> - <citations/> +The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction]]></help> + <citations> + <citation type="doi">10.1007/s00239-005-0027-1</citation> + </citations> </tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml --- a/tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="MET4J_VERSION_TEST">\n- <description>Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology</description>\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="develop">\n+ <description>Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath"\n #if str($inputSide) != \'None\':\n@@ -25,18 +25,18 @@\n ]]></command>\n <inputs>\n <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n- <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>\n- <param argument="-c" label="Selected compartment(s), as model identifiers, separated by "+" sign if more than one" name="comp" optional="true" type="text" value="">\n+ <param argument="-sc" format="txt" label="input side compound file" name="inputSide" optional="true" type="data" value=""/>\n+ <param argument="-c" label="selected compartment(s), as model identifiers, separated by "+" sign if more than one" name="comp" optional="true" type="text" value="">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n <param argument="-s" checked="false" falsevalue="" label="export seeds" name="source" truevalue="-s" type="boolean" value="false"/>\n <param argument="-t" checked="false" falsevalue="" label="export targets" name="sink" truevalue="-t" type="boolean" value="false"/>\n- <param argument="-!s" checked="false" falsevalue="" label="export nodes that are not seed" name="notsource" truevalue="-!s" type="boolean" value="false"/>\n+ <param argument="-!s" checked="false" falsevalue="" label="export nodes that are not seeds" name="notsource" truevalue="-!s" type="boolean" value="false"/>\n <param argument="-!t" checked="false" falsevalue="" label="export nodes that are not targets" name="notsink" truevalue="-!t" type="boolean" value="false"/>\n- <param argument="-is" checked="false" falsevalue="" label="do not ignore isolated nodes, consider isolated both seed and target" name="keepIsolated" truevalue="-is" type="boolean" value="false"/>\n- <param argument="-B" checked="false" falsevalue="" label="use Borenstein Algorithm. Please cite Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105). ignore internal option" name="useBorensteinAlg" truevalue="-B" type="boolean" value="false"/>\n+ <param argument="-is" checked="false" falsevalue="" label="do not ignore isolated nodes, consider isolated both seeds and targets" name="keepIsolated" truevalue="-is" type="boolean" value="false"/>\n+ <param argument="-B" checked="false" falsevalue="" label="use Borenstein Algorithm. Please cite Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105), ignore internal option" name="useBorensteinAlg" truevalue="-B" type="boolean" value="false"/>\n <param argument="-in" checked="false" falsevalue="" label="if an external compartment is defined, adjust degree by conside'..b'Path">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_columns n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="26"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_line_matching expression="^M_\\S+_\\w" n="26"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n- <help><![CDATA[Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology. Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms.\n+ <help><![CDATA[Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology\n+Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms.\n This application can use seed definition and SCC-based detection algorithm by Borenstein et al. or, alternatively, degree-based sink and source detection with compartment adjustment.\n-The first method (see Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105) consider strongly connected components rather than individual nodes, thus, members of cycles can be considered as seed. A sink from an external compartment can however be connected to a non sink internal counterpart, thus highlighting what could end up in the external compartment rather than what must be exported.\n+The first method (see Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105) consider strongly connected components rather than individual nodes, thus, members of cycles can be considered as seeds. A sink from an external compartment can however be connected to a non sink internal counterpart, thus highlighting what could end up in the external compartment rather than what must be exported.\n The second approach is neighborhood based and identify sources and sinks. Since "real" sinks and sources in intracellular compartment(s) may be involved in transport/exchange reactions reversible by default, thus not allowing extracellular source or sink, an option allows to take the degree (minus extracellular neighbors) of intracellular counterparts.]]></help>\n- <citations/>\n+ <citations>\n+ <citation type="doi">10.1073/pnas.0806162105</citation>\n+ </citations>\n </tool>\n' |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml --- a/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="MET4J_VERSION_TEST">\n- <description>Scan a network to identify side-compounds.</description>\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="develop">\n+ <description>Scan a network to identify side compounds.</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath"\n $sideOnly\n@@ -28,18 +28,18 @@\n ]]></command>\n <inputs>\n <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n- <param argument="-s" checked="false" falsevalue="" label="output compounds flagged as side-Compounds only" name="sideOnly" truevalue="-s" type="boolean" value="false"/>\n- <param argument="-id" checked="false" falsevalue="" label="do not report values in output, export ids list of compounds flagged as side-Compounds, allowing piping results" name="noReportValue" truevalue="-id" type="boolean" value="false"/>\n- <param argument="-d" label="flag as side compounds any compounds with degree above threshold" name="degree" optional="true" type="text" value="400">\n+ <param argument="-s" checked="false" falsevalue="" label="output compounds flagged as side compounds only" name="sideOnly" truevalue="-s" type="boolean" value="false"/>\n+ <param argument="-id" checked="false" falsevalue="" label="do not report values in output, export ids of compounds flagged as side compounds, allowing piping results" name="noReportValue" truevalue="-id" type="boolean" value="false"/>\n+ <param argument="-d" label="flag as side compounds any compound with degree above threshold" name="degree" optional="true" type="text" value="400">\n <sanitizer invalid_char="_">\n <valid initial="string.printable"/>\n </sanitizer>\n </param>\n <param argument="-dp" label="flag as side compounds the top x% of compounds according to their degree" name="degreePrecentile" optional="true" type="float" value="NaN"/>\n- <param argument="-cc" checked="false" falsevalue="" label="flag as side compound any compounds with less than 2 carbons in formula" name="flagInorganic" truevalue="-cc" type="boolean" value="false"/>\n- <param argument="-uf" checked="false" falsevalue="" label="flag as side compound any compounds with no valid chemical formula" name="flagNoFormula" truevalue="-uf" type="boolean" value="false"/>\n+ <param argument="-cc" checked="false" falsevalue="" label="flag as side compound any compound with less than 2 carbons in formula" name="flagInorganic" truevalue="-cc" type="boolean" value="false"/>\n+ <param argument="-uf" checked="false" falsevalue="" label="flag as side compound any compound with no valid chemical formula" name="flagNoFormula" truevalue="-uf" type="boolean" value="false"/>\n <param argument="-nc" label="flag as side compound any compound with a number of parallel edges shared with a neighbor above the given threshold" name="parallelEdge" optional="true" type="float" value="NaN"/>\n- <param argument="-m" label="Degree is shared between compounds in different compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">\n+ <param argument="-m" label="degree is shared between compounds in different compartments. Use names i'..b'"tsv" name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="6"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_columns n="1"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n- <help><![CDATA[Scan a network to identify side-compounds.\n+ <help><![CDATA[Scan a network to identify side compounds.\n Side compounds are metabolites of small relevance for topological analysis. Their definition can be quite subjective and varies between sources.\n Side compounds tend to be ubiquitous and not specific to a particular biochemical or physiological process.Compounds usually considered as side compounds include water, atp or carbon dioxide. By being involved in many reactions and thus connected to many compounds, they tend to significantly lower the average shortest path distances beyond expected metabolic relatedness.\n This tool attempts to propose a list of side compounds according to specific criteria: \n - *Degree*: Compounds with an uncommonly high number of neighbors can betray a lack of process specificity. \n High degree compounds typically include water and most main cofactors (CoA, ATP, NADPH...) but can also include central compounds such as pyruvate or acetyl-CoA \n - *Neighbor Coupling*: Similar to degree, this criteria assume that side compounds are involved in many reactions, but in pairs with other side compounds.\n-Therefore, the transition from ATP to ADP will appear multiple time in the network, creating redundant \'parallel edges\' between these two neighbors.\n+Therefore, the transition from ATP to ADP will appear multiple times in the network, creating redundant \'parallel edges\' between these two neighbors.\n Being tightly coupled to another compound through a high number of redundant edges, can point out cofactors while keeping converging pathways\' products with high degree like pyruvate aside. \n - *Carbon Count*: Metabolic "waste", or degradation end-product such as ammonia or carbon dioxide are usually considered as side compounds.\n Most of them are inorganic compound, another ill-defined concept, sometimes defined as compound lacking C-C or C-H bonds. Since chemical structure is rarely available in SBML model beyond chemical formula, we use a less restrictive criterion by flagging compound with one or no carbons. This cover most inorganic compounds, but include few compounds such as methane usually considered as organic. - *Chemical Formula*: Metabolic network often contains \'artifacts\' that serve modelling purpose (to define a composite objective function for example). Such entities can be considered as \'side entities\'. Since they are not actual chemical compounds, they can be detected by their lack of valid chemical formula. However, this can also flag main compounds with erroneous or missing annotation.]]></help>\n' |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/networkAnalysis/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml --- a/tools/networkAnalysis/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/networkAnalysis/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| b'@@ -1,13 +1,13 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="met4j_TopologicalPathwayAnalysis" name="TopologicalPathwayAnalysis" version="MET4J_VERSION_TEST">\n- <description>Run a Topological Pathway Analysis to identify key pathways based on topological properties of its constituting compounds.</description>\n+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n+<tool id="met4j_TopologicalPathwayAnalysis" name="TopologicalPathwayAnalysis" version="develop">\n+ <description>Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds.</description>\n <xrefs>\n <xref type="bio.tools">met4j</xref>\n </xrefs>\n <requirements>\n- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>\n+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>\n </requirements>\n- <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.TopologicalPathwayAnalysis -s "$inputPath"\n+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.TopologicalPathwayAnalysis -i "$inputPath"\n #if str($inputSide) != \'None\':\n -sc "$inputSide"\n #end if\n@@ -24,7 +24,7 @@\n -o "$outputPath"\n ]]></command>\n <inputs>\n- <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n+ <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>\n <param argument="-sc" format="txt" label="input Side compound file (recommended)" name="inputSide" optional="true" type="data" value=""/>\n <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">\n <option selected="true" value="no">no</option>\n@@ -42,32 +42,297 @@\n </outputs>\n <tests>\n <test>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputPath" value="XF_network.sbml"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="dataPath" value="XF_network_C_NOI.txt"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="inputSide" value="XF_network_C_Side.tab"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_columns n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ '..b' \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="removeIsolated" value="true"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="out" value="true"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <param name="mergingStrat" value="by_id"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <output name="outputPath">\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_columns n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n <has_n_lines n="3"/>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </assert_contents>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </output>\n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n+ \n </test>\n </tests>\n- <help><![CDATA[Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its mapped compounds. From a list of compounds of interest, the app compute their betweenness centrality (which quantifies how often a compound acts as a intermediary along the shortest paths between pairs of other compounds in the network, which, if high, suggest a critical role in the overall flow within the network). Each pathway is scored according to the summed centrality of its metabolites found in the dataset. Alternatively to the betweenness, one can make use of the out-degree (the number of outgoing link, i.e. number of direct metabolic product) as a criterion of importance. TPA is complementary to statistical enrichment analysis to ensures a more meaningful interpretation of the data, by taking into account the influence of identified compounds on the structure of the pathways.]]></help>\n+ <help><![CDATA[Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds.\n+From a list of compounds of interest, the app compute their betweenness centrality (which quantifies how often a compound acts as a intermediary along the shortest paths between pairs of other compounds in the network, which, if high, suggest a critical role in the overall flow within the network). Each pathway is scored according to the summed centrality of its metabolites found in the dataset. Alternatively to the betweenness, one can make use of the out-degree (the number of outgoing link, i.e. number of direct metabolic product) as a criterion of importance. TPA is complementary to statistical enrichment analysis to ensures a more meaningful interpretation of the data, by taking into account the influence of identified compounds on the structure of the pathways.]]></help>\n <citations/>\n </tool>\n' |
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| diff -r 1274e2a62479 -r 0976a6257300 tools/reconstruction/CreateMetaNetwork/CreateMetaNetwork.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/reconstruction/CreateMetaNetwork/CreateMetaNetwork.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -0,0 +1,210 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="develop"> + <description>Create a Meta-Network from two sub-networks in SBML format.</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath" + -n2 "$sbml2FilePath" + -n1ex "$external1" + -n2ex "$external2" +#if str($n1prefix): + -n1px "$n1prefix" +#end if +#if str($n2prefix): + -n2px "$n2prefix" +#end if + $keepCompartment + $firstIsMeta +#if str($mergingCriterion): + -mc "$mergingCriterion" +#end if + -o "$outputPath" +]]></command> + <inputs> + <param argument="-n1" format="sbml" label="input SBML file: path to first network, in sbml format." name="sbml1FilePath" optional="false" type="data" value=""/> + <param argument="-n2" format="" label="input SBML file: path to second network, in sbml format." name="sbml2FilePath" optional="false" type="data" value=""/> + <param argument="-n1ex" label="external compartment identifier in first network." name="external1" optional="false" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-n2ex" label="external compartment identifier in second network." name="external2" optional="false" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-n1px" label="prefix that will be added to first network's entities identifiers" name="n1prefix" optional="true" type="text" value="Net1_"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-n2px" label="prefix that will be added to second network's entities identifiers" name="n2prefix" optional="true" type="text" value="Net2_"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-k" checked="false" falsevalue="" label="keep the original external compartments in the meta-network, otherwise, they will be fused into the new shared external compartment" name="keepCompartment" truevalue="-k" type="boolean" value="false"/> + <param argument="-n1meta" checked="false" falsevalue="" label="treat first network as meta-network, allowing more than two sub-models with iterative fusions. This will overwrite shared compartment and pool compounds (which must follow the "pool_" prefix convention) and will ignore --n1prefix argument" name="firstIsMeta" truevalue="-n1meta" type="boolean" value="false"/> + <param argument="-mc" label="field used to identify the same metabolites across the two different networks. "by_name"/"by_id" can be used if names/identifiers are consistent and unambiguous across source models, "by_metanetx" can be used if models contains MetaNetX identifiers in annotation field using standard miriam format." name="mergingCriterion" optional="true" type="select" value="by_name"> + <option value="by_metanetx">by_metanetx</option> + <option selected="true" value="by_name">by_name</option> + <option value="by_id">by_id</option> + </param> + </inputs> + <outputs> + <data format="sbml" name="outputPath"/> + </outputs> + <tests> + <test> + + + + + + + + + + + <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/> + + + + + + + + + + + <param name="sbml2FilePath" value="ECOL.xml"/> + + + + + + + + + + + <param name="external1" value="s"/> + + + + + + + + + + + <param name="external2" value="e"/> + + + + + + + + + + + <param name="n1prefix" value="hsa"/> + + + + + + + + + + + <param name="n2prefix" value="eco"/> + + + + + + + + + + + <param name="mergingCriterion" value="by_metanetx"/> + + + + + + + + + + + <output ftype="sbml" name="outputPath"> + + + + + + + + + + + <assert_contents> + + + + + + + + + + + <has_text text="</sbml>"/> + + + + + + + + + + + </assert_contents> + + + + + + + + + + + </output> + + + + + + + + + + + </test> + </tests> + <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format. +A meta-network is a single model which contains several sub-networks that remains individualized within the meta-network (as opposed to model fusion), but which can share some of their components with other sub-networks through a shared "medium" compartment.]]></help> + <citations/> +</tool> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/reconstruction/CreateMetaNetwork/test-data/ECOL.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/reconstruction/CreateMetaNetwork/test-data/ECOL.xml Fri Jan 31 18:28:53 2025 +0000 |
| b |
| b'@@ -0,0 +1,138833 @@\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="iML1515" metaid="iML1515" name="Escherichia coli str. K-12 substr. MG1655">\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="#iML1515">\r\n+ <bqbiol:hasProperty>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/pubmed/29020004"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/taxonomy/511145"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:hasProperty>\r\n+ <bqbiol:is>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/bigg.model/iML1515"/>\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_Ec_iML1515_core_75p37M"/>\r\n+ </fbc:listOfFluxObjectives>\r\n+ </fbc:objective>\r\n+ </fbc:listOfObjectives>\r\n+ <fbc:listOfGeneProducts>\r\n+ <fbc:geneProduct fbc:id="b4054" fbc:label="b4054" fbc:name="b4054" metaid="_19a85f06-f4d2-4ca4-962d-280d860d0188"/>\r\n+ <fbc:geneProduct fbc:id="b4053" fbc:label="b4053" fbc:name="b4053" metaid="_3320c40d-844a-45b2-a996-49c250766d53"/>\r\n+ <fbc:geneProduct fbc:id="b4298" fbc:label="b4298" fbc:name="b4298" metaid="_428fe2b1-ed44-4ef1-a55e-e9a88f70e43c"/>\r\n+ <fbc:geneProduct fbc:id="b4055" fbc:label="b4055" fbc:name="b4055" metaid="d3169d49-b4b4-439a-ba53-bb6292583779"/>\r\n+ <fbc:geneProduct fbc:id="b4297" fbc:label="b4297" fbc:name="b4297" metaid="_388e6eb0-5734-4c6e-9ef3-b927d0ee6f80"/>\r\n+ <fbc:geneProduct fbc:id="b4291" fbc:label="b4291" fbc:name="b4291" metaid="_9dd0f62e-2f14-4bef-b52a-262c735f727e"/>\r\n+ <fbc:geneProduct fbc:id="b0929" fbc:label="b0929" fbc:name="b0929" metaid="_337058ef-dd29-4e6e-861b-0c9a3c8ca11e"/>\r\n+ <fbc:geneProduct fbc:id="b0928" fbc:label="b0928" fbc:name="b0928" metaid="_2442f6a8-23e0-4e7d-99d6-3231f1260af1"/>\r\n+ <fbc:geneProduct fbc:id="b4290" fbc:label="b4290" fbc:name="b4290" metaid="cb5b0ae1-c107-4e9d-87bb-ca77a4e3d321"/>\r\n+ <fbc:geneProduct fbc:id="b0925" fbc:label="b0925" fbc:name="b0925" metaid="_80d0d7b3-f687-4841-8710-c3fe1788eb09"/>\r\n+ <fbc:geneProduct fbc:id="b4289" fbc:label="b4289" fbc:name="b4289" metaid="_813528ea-ec16-47fe-87cb-9dec6c6b78e2"/>\r\n+ <fbc:geneProduct fbc:id="b3199" fbc:label="b3199" fbc:name="b3199" metaid="_691a4ce9-01cd-4521-9e44-ae134a3d2a7f"/>\r\n+ <fbc:geneProduct fbc:id="b4288" fbc:label="b4288" fbc:name="b4288" metaid="fe7c001f-5b97-4a68-b421-36b27339b0dd"/>\r\n+ <fbc:geneProduct fbc:id="b4042" fbc:label="b4042" fbc:name="b4042" metaid="a9592745-8729-473a-9cb6-d5827d734dda"/>\r\n+ <fbc:geneProduct fbc:id="b3196" fbc:label="b3196" fbc:name="b3196" metaid="fd61ed6b-3ce6-42c8-ac48-d8ea58fc2bac"/>\r\n+ <fbc:geneProduct fbc:id="b3197" fbc:label="b3197" fbc:name="b3197" metaid="c9c8d396-7abc-4f97-8994-3a3e334ed6b1"/>\r\n+ <fbc:geneProduct fbc:id="b4287" fbc:label="b4287" fbc:name="b4287" metaid="c7589f3b-726a-4909-9514-d9eb40ef6815"/>\r\n+ <fbc:geneProduct fbc:id="b3198" fbc:label="b3198" fbc:name="b3198" metaid="bc09d6b2-a4bc-463c-bec4-8cfa2dd246cd"/>\r\n+ <fbc:geneProduct fbc:id="b4041" fbc:label="b4041" fbc:name="b4041" metaid="_94a9500a-9cb8-471a-960c-ed3dd82df137"/>\r\n+ <fbc:geneProduct fbc:id="b4040" fbc:label="b4040" fbc:name="b4040" metaid="_5f93eaf9-e592-4529-bb84-f8662'..b'tAssociation>\r\n+ <listOfReactants>\r\n+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1"/>\r\n+ </listOfReactants>\r\n+ <listOfProducts>\r\n+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_h_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_ggptrc_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>\r\n+ </listOfProducts>\r\n+ </reaction>\r\n+ <reaction fbc:lowerFluxBound="LOWER_BOUND_1000_0" fbc:upperFluxBound="UPPER_BOUND_1000_0" id="R_ARBtex" metaid="b50bec2f-a0bc-4dbb-af50-60907396df82" name="L-arabinose transport via diffusion (extracellular to periplasm)" reversible="true" sboTerm="SBO:0000185">\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="#b50bec2f-a0bc-4dbb-af50-60907396df82">\r\n+ <bqbiol:is>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR95913"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ARBtex"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:is>\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="b1377"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="b0929"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="b0241"/>\r\n+ <fbc:geneProductRef fbc:geneProduct="b2215"/>\r\n+ </fbc:or>\r\n+ </fbc:geneProductAssociation>\r\n+ <listOfReactants>\r\n+ <speciesReference constant="true" species="M_arab__L_e" stoichiometry="1"/>\r\n+ </listOfReactants>\r\n+ <listOfProducts>\r\n+ <speciesReference constant="true" species="M_arab__L_p" 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_FACOAE120" metaid="_50a8274a-ed7a-4669-a5cf-95aa9824ac76" name="Fatty-acid-CoA thioesterase (dodecanoate)" reversible="false" sboTerm="SBO:0000176">\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="#_50a8274a-ed7a-4669-a5cf-95aa9824ac76">\r\n+ <bqbiol:is>\r\n+ <rdf:Bag>\r\n+ <rdf:li rdf:resource="https://identifiers.org/ec-code/3.1.2.2"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR99128"/>\r\n+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FACOAE120"/>\r\n+ </rdf:Bag>\r\n+ </bqbiol:is>\r\n+ </rdf:Description>\r\n+ </rdf:RDF>\r\n+ </annotation>\r\n+ <fbc:geneProductAssociation>\r\n+ <fbc:geneProductRef fbc:geneProduct="b0452"/>\r\n+ </fbc:geneProductAssociation>\r\n+ <listOfReactants>\r\n+ <speciesReference constant="true" species="M_ddcacoa_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1"/>\r\n+ </listOfReactants>\r\n+ <listOfProducts>\r\n+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_h_c" stoichiometry="1"/>\r\n+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>\r\n+ </listOfProducts>\r\n+ </reaction>\r\n+ </listOfReactions>\r\n+ </model>\r\n+</sbml>\r\n' |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/reconstruction/CreateMetaNetwork/test-data/Human-GEM_pathways.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/reconstruction/CreateMetaNetwork/test-data/Human-GEM_pathways.xml Fri Jan 31 18:28:53 2025 +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 1274e2a62479 -r 0976a6257300 tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml --- a/tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml Fri Jan 31 18:28:53 2025 +0000 |
| [ |
| @@ -1,17 +1,17 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="MET4J_VERSION_TEST"> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="develop"> <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:MET4J_VERSION_TEST</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> </requirements> - <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.SbmlCheckBalance -sbml "$sbml" + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.SbmlCheckBalance -i "$sbml" -out "$out" ]]></command> <inputs> - <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> + <param argument="-i" format="sbml" label="Input Sbml file" name="sbml" optional="false" type="data" value=""/> </inputs> <outputs> <data format="tsv" name="out"/> |
| b |
| diff -r 1274e2a62479 -r 0976a6257300 tools/tool_conf.xml --- a/tools/tool_conf.xml Wed Jul 26 15:33:45 2023 +0000 +++ b/tools/tool_conf.xml Fri Jan 31 18:28:53 2025 +0000 |
| b |
| @@ -1,39 +1,40 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version="1.0" encoding="UTF-8" standalone="no"?> <toolbox monitor="true"> <label id="met4j" text="MET4J"/> <section id="met4j_attributes" name="Met4J - attributes"/> - <tool file="met4j/attributes/DecomposeSBML/DecomposeSBML.xml"/> + <tool file="met4j/attributes/ExtractAnnotations/ExtractAnnotations.xml"/> <tool file="met4j/attributes/ExtractPathways/ExtractPathways.xml"/> - <tool file="met4j/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml"/> + <tool file="met4j/attributes/GetEntities/GetEntities.xml"/> <tool file="met4j/attributes/GetGenesFromReactions/GetGenesFromReactions.xml"/> + <tool file="met4j/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml"/> <tool file="met4j/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml"/> - <tool file="met4j/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml"/> - <tool file="met4j/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml"/> - <tool file="met4j/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml"/> - <tool file="met4j/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml"/> - <tool file="met4j/attributes/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml"/> - <tool file="met4j/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml"/> - <tool file="met4j/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml"/> - <tool file="met4j/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml"/> - <tool file="met4j/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml"/> + <tool file="met4j/attributes/SetCharges/SetCharges.xml"/> + <tool file="met4j/attributes/SetChemicalFormulas/SetChemicalFormulas.xml"/> + <tool file="met4j/attributes/SetEcNumbers/SetEcNumbers.xml"/> + <tool file="met4j/attributes/SetGprs/SetGprs.xml"/> + <tool file="met4j/attributes/SetIds/SetIds.xml"/> + <tool file="met4j/attributes/SetNames/SetNames.xml"/> + <tool file="met4j/attributes/SetPathways/SetPathways.xml"/> + <tool file="met4j/attributes/SetReferences/SetReferences.xml"/> <section id="met4j_bigg" name="Met4J - bigg"/> - <tool file="met4j/bigg/GetModelProteome/GetModelProteome.xml"/> + <tool file="met4j/bigg/GetBiggModelProteome/GetBiggModelProteome.xml"/> <section id="met4j_convert" name="Met4J - convert"/> <tool file="met4j/convert/FbcToNotes/FbcToNotes.xml"/> <tool file="met4j/convert/Kegg2Sbml/Kegg2Sbml.xml"/> - <tool file="met4j/convert/SBMLwizard/SBMLwizard.xml"/> + <tool file="met4j/convert/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml"/> + <tool file="met4j/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml"/> <tool file="met4j/convert/Sbml2Graph/Sbml2Graph.xml"/> + <tool file="met4j/convert/Sbml2PathwayNet/Sbml2PathwayNet.xml"/> <tool file="met4j/convert/Sbml2Tab/Sbml2Tab.xml"/> + <tool file="met4j/convert/SbmlWizard/SbmlWizard.xml"/> <tool file="met4j/convert/Tab2Sbml/Tab2Sbml.xml"/> <section id="met4j_mapping" name="Met4J - mapping"/> <tool file="met4j/mapping/NameMatcher/NameMatcher.xml"/> <tool file="met4j/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml"/> <section id="met4j_networkanalysis" name="Met4J - networkAnalysis"/> <tool file="met4j/networkAnalysis/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml"/> - <tool file="met4j/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml"/> <tool file="met4j/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml"/> <tool file="met4j/networkAnalysis/ChokePoint/ChokePoint.xml"/> - <tool file="met4j/networkAnalysis/CompoundNet/CompoundNet.xml"/> <tool file="met4j/networkAnalysis/DegreeWeighting/DegreeWeighting.xml"/> <tool file="met4j/networkAnalysis/DistanceMatrix/DistanceMatrix.xml"/> <tool file="met4j/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml"/> @@ -42,7 +43,6 @@ <tool file="met4j/networkAnalysis/LoadPoint/LoadPoint.xml"/> <tool file="met4j/networkAnalysis/MetaboRank/MetaboRank.xml"/> <tool file="met4j/networkAnalysis/NetworkSummary/NetworkSummary.xml"/> - <tool file="met4j/networkAnalysis/PathwayNet/PathwayNet.xml"/> <tool file="met4j/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml"/> <tool file="met4j/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml"/> <tool file="met4j/networkAnalysis/ScopeNetwork/ScopeNetwork.xml"/> @@ -50,5 +50,6 @@ <tool file="met4j/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml"/> <tool file="met4j/networkAnalysis/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml"/> <section id="met4j_reconstruction" name="Met4J - reconstruction"/> + <tool file="met4j/reconstruction/CreateMetaNetwork/CreateMetaNetwork.xml"/> <tool file="met4j/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml"/> </toolbox> |