| Previous changeset 10:6a112eaf8f38 (2025-02-03) |
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Commit message:
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518 |
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modified:
build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml build/tools/ChokePoint/ChokePoint.xml build/tools/CreateMetaNetwork/CreateMetaNetwork.xml build/tools/DegreeWeighting/DegreeWeighting.xml build/tools/DistanceMatrix/DistanceMatrix.xml build/tools/ExtractAnnotations/ExtractAnnotations.xml build/tools/ExtractPathways/ExtractPathways.xml build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml build/tools/ExtractSubNetwork/ExtractSubNetwork.xml build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml build/tools/FbcToNotes/FbcToNotes.xml build/tools/GetBiggModelProteome/GetBiggModelProteome.xml build/tools/GetEntities/GetEntities.xml build/tools/GetGenesFromReactions/GetGenesFromReactions.xml build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.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/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml build/tools/Sbml2Graph/Sbml2Graph.xml build/tools/Sbml2PathwayNet/Sbml2PathwayNet.xml build/tools/Sbml2Tab/Sbml2Tab.xml build/tools/SbmlCheckBalance/SbmlCheckBalance.xml build/tools/SbmlWizard/SbmlWizard.xml build/tools/ScopeNetwork/ScopeNetwork.xml build/tools/SeedsAndTargets/SeedsAndTargets.xml build/tools/SetCharges/SetCharges.xml build/tools/SetChemicalFormulas/SetChemicalFormulas.xml build/tools/SetEcNumbers/SetEcNumbers.xml build/tools/SetGprs/SetGprs.xml build/tools/SetIds/SetIds.xml build/tools/SetNames/SetNames.xml build/tools/SetPathways/SetPathways.xml build/tools/SetReferences/SetReferences.xml build/tools/SideCompoundsScan/SideCompoundsScan.xml build/tools/Tab2Sbml/Tab2Sbml.xml build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml tests.html tools/attributes/ExtractAnnotations/ExtractAnnotations.xml tools/attributes/ExtractPathways/ExtractPathways.xml tools/attributes/GetEntities/GetEntities.xml tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml tools/attributes/SetCharges/SetCharges.xml tools/attributes/SetChemicalFormulas/SetChemicalFormulas.xml tools/attributes/SetEcNumbers/SetEcNumbers.xml tools/attributes/SetGprs/SetGprs.xml tools/attributes/SetIds/SetIds.xml tools/attributes/SetNames/SetNames.xml tools/attributes/SetPathways/SetPathways.xml tools/attributes/SetReferences/SetReferences.xml tools/bigg/GetBiggModelProteome/GetBiggModelProteome.xml tools/convert/FbcToNotes/FbcToNotes.xml tools/convert/Kegg2Sbml/Kegg2Sbml.xml tools/convert/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml tools/convert/Sbml2Graph/Sbml2Graph.xml tools/convert/Sbml2PathwayNet/Sbml2PathwayNet.xml tools/convert/Sbml2Tab/Sbml2Tab.xml tools/convert/SbmlWizard/SbmlWizard.xml tools/convert/Tab2Sbml/Tab2Sbml.xml tools/mapping/NameMatcher/NameMatcher.xml tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml 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/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/CreateMetaNetwork/CreateMetaNetwork.xml tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml --- a/build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="2.0.0"> +<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.BipartiteDistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml --- a/build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="2.0.0"> +<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type): -f "$type" @@ -68,7 +68,7 @@ <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/btu760</citation> <citation type="doi">10.1093/bioinformatics/bti116</citation> - <citation type="doi">10.1093/bioinformatics/btu760</citation> </citations> </tool> |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ChokePoint/ChokePoint.xml --- a/build/tools/ChokePoint/ChokePoint.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ChokePoint/ChokePoint.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ChokePoint" name="ChokePoint" version="2.0.0"> +<tool id="met4j_ChokePoint" name="ChokePoint" version="2.0.1"> <description>Compute the Choke points of a metabolic network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath" -o "$outputPath" @@ -18,15 +18,25 @@ </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> </tests> <help><![CDATA[Compute the Choke points of a metabolic network. |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/CreateMetaNetwork/CreateMetaNetwork.xml --- a/build/tools/CreateMetaNetwork/CreateMetaNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/CreateMetaNetwork/CreateMetaNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.0"> +<tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath" -n2 "$sbml2FilePath" @@ -60,18 +60,31 @@ </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. |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/DegreeWeighting/DegreeWeighting.xml --- a/build/tools/DegreeWeighting/DegreeWeighting.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/DegreeWeighting/DegreeWeighting.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="2.0.0"> +<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DegreeWeighting#if str($pow): -pow "$pow" |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/DistanceMatrix/DistanceMatrix.xml --- a/build/tools/DistanceMatrix/DistanceMatrix.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/DistanceMatrix/DistanceMatrix.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="2.0.0"> +<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="2.0.1"> <description>Create a compound to compound distance matrix.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -34,30 +34,54 @@ </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. |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ExtractAnnotations/ExtractAnnotations.xml --- a/build/tools/ExtractAnnotations/ExtractAnnotations.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ExtractAnnotations/ExtractAnnotations.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="2.0.0"> +<tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="2.0.1"> <description>Extract databases' references from SBML annotations or notes.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractAnnotations -i "$inputPath" -export "$export" @@ -34,40 +34,73 @@ </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> |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ExtractPathways/ExtractPathways.xml --- a/build/tools/ExtractPathways/ExtractPathways.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ExtractPathways/ExtractPathways.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractPathways" name="ExtractPathways" version="2.0.0"> +<tool id="met4j_ExtractPathways" name="ExtractPathways" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath" -p "$pathwayId" @@ -24,15 +24,25 @@ </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> + </test> </tests> <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file]]></help> |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml --- a/build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="2.0.0"> +<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath" -s "$sourcePath" @@ -54,17 +54,29 @@ </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"/> + <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 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. |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ExtractSubNetwork/ExtractSubNetwork.xml --- a/build/tools/ExtractSubNetwork/ExtractSubNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ExtractSubNetwork/ExtractSubNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="2.0.0"> +<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath" -s "$sourcePath" @@ -56,29 +56,41 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="sourcePath" value="seeds.txt"/> + <param name="targetPath" value="targets.txt"/> + <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 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.]]></help> <citations> + <citation type="doi">10.1093/nar/gki437</citation> + <citation type="doi">10.1093/bioinformatics/btg217</citation> <citation type="doi">10.1093/bib/bbv115</citation> <citation type="doi">10.1016/j.biosystems.2011.05.004</citation> + <citation type="doi">10.1093/bioinformatics/bti116</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> |
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| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml --- a/build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="2.0.0"> +<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath" -s "$sourcePath" @@ -54,17 +54,29 @@ </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"/> + <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 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. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/FbcToNotes/FbcToNotes.xml --- a/build/tools/FbcToNotes/FbcToNotes.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/FbcToNotes/FbcToNotes.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_FbcToNotes" name="FbcToNotes" version="2.0.0"> +<tool id="met4j_FbcToNotes" name="FbcToNotes" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath" -o "$outputPath" @@ -18,13 +18,21 @@ </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 html notes (see https://www.degruyter.com/document/doi/10.1515/jib-2017-0082/html)]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/GetBiggModelProteome/GetBiggModelProteome.xml --- a/build/tools/GetBiggModelProteome/GetBiggModelProteome.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/GetBiggModelProteome/GetBiggModelProteome.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="2.0.0"> +<tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetBiggModelProteome -m "$modelId" -o "$outputFile" @@ -22,12 +22,19 @@ </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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/GetEntities/GetEntities.xml --- a/build/tools/GetEntities/GetEntities.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/GetEntities/GetEntities.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetEntities" name="GetEntities" version="2.0.0"> +<tool id="met4j_GetEntities" name="GetEntities" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetEntities -i "$sbml" $printMetabolites @@ -30,29 +30,52 @@ </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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/GetGenesFromReactions/GetGenesFromReactions.xml --- a/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.0"> +<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml" -r "$reactionFile" @@ -34,15 +34,25 @@ </outputs> <tests> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_n_lines n="2"/> + <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> + <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.xml --- a/build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="2.0.0"> +<tool id="met4j_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="2.0.1"> <description>Create a tabulated file with metabolite attributes from a SBML file</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetMetaboliteAttributes -i "$sbml" -o "$outputFile" @@ -18,15 +18,25 @@ </outputs> <tests> <test> + <param name="sbml" value="toy_model.xml"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_n_lines n="9"/> + <has_n_columns n="6"/> + <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/> + <has_line_matching expression=".*C.*NC.*" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml --- a/build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/GetReactantsFromReactions/GetReactantsFromReactions.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="2.0.0"> +<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="2.0.1"> <description>Get reactant lists from a list of reactions and a SBML file.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetReactantsFromReactions -i "$sbml" -r "$reactionFile" @@ -38,36 +38,65 @@ </outputs> <tests> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_text_matching expression="R_GLUN" n="4"/> + <has_text_matching expression="R_ACGS" n="5"/> + </assert_contents> + </output> + </test> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + <param name="printSubstrates" value="true"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_text_matching expression="R_GLUN" n="2"/> + <has_text_matching expression="R_ACGS" n="5"/> + </assert_contents> + </output> + </test> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + <param name="printProducts" value="true"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_text_matching expression="R_GLUN" n="2"/> + <has_text_matching expression="R_ACGS" n="5"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Get 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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/Kegg2Sbml/Kegg2Sbml.xml --- a/build/tools/Kegg2Sbml/Kegg2Sbml.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/Kegg2Sbml/Kegg2Sbml.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="2.0.0"> +<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="2.0.1"> <description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org): -org "$org" |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/LoadPoint/LoadPoint.xml --- a/build/tools/LoadPoint/LoadPoint.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/LoadPoint/LoadPoint.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_LoadPoint" name="LoadPoint" version="2.0.0"> +<tool id="met4j_LoadPoint" name="LoadPoint" version="2.0.1"> <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -30,13 +30,21 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="8"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/MetaboRank/MetaboRank.xml --- a/build/tools/MetaboRank/MetaboRank.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/MetaboRank/MetaboRank.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_MetaboRank" name="MetaboRank" version="2.0.0"> +<tool id="met4j_MetaboRank" name="MetaboRank" version="2.0.1"> <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath" -s "$seedsFilePath" @@ -44,15 +44,25 @@ </outputs> <tests> <test> + <param name="sbmlFilePath" value="XF_network.sbml"/> + <param name="seedsFilePath" value="XF_network_C_Seed.tab"/> + <param name="inputSide" value="XF_network_C_Side.tab"/> + <output name="output"> + <assert_contents> + <has_n_lines n="1100"/> + <has_n_columns n="11"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/NameMatcher/NameMatcher.xml --- a/build/tools/NameMatcher/NameMatcher.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/NameMatcher/NameMatcher.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_NameMatcher" name="NameMatcher" version="2.0.0"> +<tool id="met4j_NameMatcher" name="NameMatcher" version="2.0.1"> <description>This tool runs edit-distance based fuzzy matching to perform near-similar name matching between a metabolic model and a list of chemical names in a dataset. A harmonization processing is performed on chemical names with substitutions of common patterns among synonyms, in order to create aliases on which classical fuzzy matching can be run efficiently.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.NameMatcher#if str($n): -nMatch "$n" @@ -60,6 +60,7 @@ </outputs> <tests/> <help><![CDATA[Metabolic models and Metabolomics Data often refer compounds only by using their common names, which vary greatly according to the source, thus impeding interoperability between models, databases and experimental data. This requires a tedious step of manual mapping. Fuzzy matching is a range of methods which can potentially helps fasten this process, by allowing the search for near-similar names. Fuzzy matching is primarily designed for common language search engines and is frequently based on edit distance, i.e. the number of edits to transform a character string into another, effectively managing typo, case and special character variations, and allowing auto-completion. However, edit-distance based search fall short when mapping chemical names: As an example, alpha-D-Glucose et Glucose would require more edits than between Fructose and Glucose. + 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.]]></help> <citations/> </tool> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/NetworkSummary/NetworkSummary.xml --- a/build/tools/NetworkSummary/NetworkSummary.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/NetworkSummary/NetworkSummary.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_NetworkSummary" name="NetworkSummary" version="2.0.0"> +<tool id="met4j_NetworkSummary" name="NetworkSummary" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -26,12 +26,19 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <output name="outputPath"> + <assert_contents> + <has_n_lines min="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a report summarizing several graph measures characterising the structure of a metabolic network. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ORApathwayEnrichment/ORApathwayEnrichment.xml --- a/build/tools/ORApathwayEnrichment/ORApathwayEnrichment.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ORApathwayEnrichment/ORApathwayEnrichment.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="2.0.0"> +<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="2.0.1"> <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != 'nan': -th "$th" @@ -32,39 +32,62 @@ </outputs> <tests> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="input" value="XF_network_C_NOI.txt"/> + <output name="outputFile"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="3"/> + </assert_contents> + </output> + </test> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="input" value="XF_network_C_NOI.txt"/> + <param name="corr" value="HolmBonferroni"/> + <param name="th" value="0.005"/> + <output name="outputFile"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="2"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test. The fisher exact test computes the probability p to randomly get the given set of values. This version computes the probability to get at least the given overlap between the given set and the given modality : Sum the hypergeometric probability with increasing target/query intersection cardinality. + The hypergeometric probability is computed from the following contingency table entries. (values in cells correspond to the marginal totals of each intersection groups) Query !Query Target a b !Target c d + The probability of obtaining the set of value is computed as following: p = ((a+b)!(c+d)!(a+c)!(b+d)!)/(a!b!c!d!(a+b+c+d)!) + The obtained p-value is then adjusted for multiple testing using one of the following methods: - Bonferroni: adjusted p-value = p*n - Benjamini-Hochberg: adjusted p-value = p*n/k |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/PrecursorNetwork/PrecursorNetwork.xml --- a/build/tools/PrecursorNetwork/PrecursorNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/PrecursorNetwork/PrecursorNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="2.0.0"> +<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="2.0.1"> <description>Perform a network expansion from a set of compound targets to create a precursor network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" -t "$targetsFilePath" @@ -38,15 +38,25 @@ </outputs> <tests> <test> + <param name="sbmlFilePath" value="toy_model.xml"/> + <param name="targetsFilePath" value="targets.txt"/> + <param name="format" value="gml"/> + <output ftype="txt" name="output"> + <assert_contents> + <has_line_matching expression=".*node.*" n="13"/> + <has_line_matching expression=".*edge.*" n="15"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml --- a/build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="2.0.0"> +<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="2.0.1"> <description>Create a reaction to reaction distance matrix.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -38,91 +38,172 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="8"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/> + <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="undirected" value="true"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="8"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/> + <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="undirected" value="true"/> + <param name="sideCompoundFile" value="sides.txt"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="8"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/> + <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/> + <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/> + <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="undirected" value="true"/> + <param name="rExclude" value="rexclude.txt"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="6"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/> + <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/> + <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/> + <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="undirected" value="true"/> + <param name="sideCompoundFile" value="sides.txt"/> + <param name="rExclude" value="rexclude.txt"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="6"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/> + <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/> + <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="sideCompoundFile" value="sides.txt"/> + <param name="rExclude" value="rexclude.txt"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="6"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/> + <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/> + <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a reaction to reaction distance matrix. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml --- a/build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="2.0.0"> +<tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="2.0.1"> <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CarbonSkeletonNet -i "$inputPath" -g "$inputAAM" @@ -46,90 +46,168 @@ </outputs> <tests> <test> + <param name="inputPath" value="Human-GEM_pathways.xml"/> + <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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="format" value="matrix"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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 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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml --- a/build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.0"> +<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.1"> <description>Advanced creation of a compound graph representation of a SBML file content</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CompoundGraph -i "$inputPath" #if str($inputSide) != 'None': @@ -54,31 +54,56 @@ </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. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/Sbml2Graph/Sbml2Graph.xml --- a/build/tools/Sbml2Graph/Sbml2Graph.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/Sbml2Graph/Sbml2Graph.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="2.0.0"> +<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="2.0.1"> <description>Create a graph representation of a SBML file content, and export it in graph file format.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" $bipartite @@ -34,38 +34,69 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="format" value="gml"/> + <output name="output"> + <assert_contents> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <assert_contents> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <assert_contents> + <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. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/Sbml2PathwayNet/Sbml2PathwayNet.xml --- a/build/tools/Sbml2PathwayNet/Sbml2PathwayNet.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/Sbml2PathwayNet/Sbml2PathwayNet.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2PathwayNet" name="Sbml2PathwayNet" version="2.0.0"> +<tool id="met4j_Sbml2PathwayNet" name="Sbml2PathwayNet" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2PathwayNet -i "$inputPath" #if str($inputSide) != 'None': |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/Sbml2Tab/Sbml2Tab.xml --- a/build/tools/Sbml2Tab/Sbml2Tab.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/Sbml2Tab/Sbml2Tab.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.0"> +<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.1"> <description>Create a tabulated file listing reaction attributes from a SBML file</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): -irr "$i" @@ -34,28 +34,50 @@ </outputs> <tests> <test> + <param name="in" value="toy_model.xml"/> + <output ftype="tsv" name="out"> + <assert_contents> + <has_n_lines n="8"/> + <has_n_columns n="9"/> + <has_text text="2.0 E[c] --> D[c]"/> + <has_text text="A[c] <==> B[c]"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model.xml"/> + <param name="i" value="->"/> + <param name="r" value="="/> + <output ftype="tsv" name="out"> + <assert_contents> + <has_n_lines n="8"/> + <has_n_columns n="9"/> + <has_text text="2.0 E[c] -> D[c]"/> + <has_text text="A[c] = B[c]"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SbmlCheckBalance/SbmlCheckBalance.xml --- a/build/tools/SbmlCheckBalance/SbmlCheckBalance.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SbmlCheckBalance/SbmlCheckBalance.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="2.0.0"> +<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="2.0.1"> <description>Check balance of all the reactions in a SBML.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.SbmlCheckBalance -i "$sbml" -out "$out" |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SbmlWizard/SbmlWizard.xml --- a/build/tools/SbmlWizard/SbmlWizard.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SbmlWizard/SbmlWizard.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.0"> +<tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.1"> <description>General SBML model processing</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath" #if str($inputSide) != 'None': @@ -56,30 +56,54 @@ </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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/ScopeNetwork/ScopeNetwork.xml --- a/build/tools/ScopeNetwork/ScopeNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/ScopeNetwork/ScopeNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="2.0.0"> +<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="2.0.1"> <description>Perform a network expansion from a set of compound seeds to create a scope network</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath" -s "$seedsFilePath" @@ -42,16 +42,27 @@ </outputs> <tests> <test> + <param name="sbmlFilePath" value="toy_model.xml"/> + <param name="seedsFilePath" value="seeds.txt"/> + <param name="sideCompoundFile" value="sides.txt"/> + <param name="format" value="gml"/> + <output ftype="txt" name="output"> + <assert_contents> + <has_line_matching expression=".*node.*" n="9"/> + <has_line_matching expression=".*edge.*" n="11"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SeedsAndTargets/SeedsAndTargets.xml --- a/build/tools/SeedsAndTargets/SeedsAndTargets.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SeedsAndTargets/SeedsAndTargets.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="2.0.0"> +<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="2.0.1"> <description>Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath" #if str($inputSide) != 'None': @@ -44,41 +44,75 @@ </outputs> <tests> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="source" value="true"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_columns n="1"/> + <has_n_lines n="109"/> + <has_line_matching expression="M_\S+_\w" n="109"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="sink" value="true"/> + <param name="useInternal" value="true"/> + <param name="comp" value="e"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_columns n="1"/> + <has_n_lines n="5"/> + <has_line_matching expression="^M_\S+_\w" n="5"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="sink" value="true"/> + <param name="useBorensteinAlg" value="true"/> + <param name="comp" value="e"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_columns n="1"/> + <has_n_lines n="26"/> + <has_line_matching expression="^M_\S+_\w" n="26"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SetCharges/SetCharges.xml --- a/build/tools/SetCharges/SetCharges.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SetCharges/SetCharges.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetCharges" name="SetCharges" version="2.0.0"> +<tool id="met4j_SetCharges" name="SetCharges" version="2.0.1"> <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetCharges#if str($colcharge) != 'nan': -cc "$colcharge" @@ -50,63 +50,117 @@ </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 metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SetChemicalFormulas/SetChemicalFormulas.xml --- a/build/tools/SetChemicalFormulas/SetChemicalFormulas.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SetChemicalFormulas/SetChemicalFormulas.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="2.0.0"> +<tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="2.0.1"> <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetChemicalFormulas#if str($colformula) != 'nan': -cf "$colformula" @@ -50,19 +50,32 @@ </outputs> <tests> <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="formula.tsv"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*CH6O6.*" n="2"/> + <has_line_matching expression=".*CH12O4.*" n="2"/> + </assert_contents> + </output> + </test> <test expect_failure="true"> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="formulaBad.tsv"/> + </test> </tests> <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SetEcNumbers/SetEcNumbers.xml --- a/build/tools/SetEcNumbers/SetEcNumbers.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SetEcNumbers/SetEcNumbers.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetEcNumbers" name="SetEcNumbers" version="2.0.0"> +<tool id="met4j_SetEcNumbers" name="SetEcNumbers" version="2.0.1"> <description>Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetEcNumbers#if str($colec) != 'nan': -cec "$colec" @@ -48,19 +48,32 @@ </outputs> <tests> <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="ec.tsv"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*1.1.1.1.*" n="2"/> + <has_line_matching expression=".*1.2.3.4.*" n="2"/> + </assert_contents> + </output> + </test> <test expect_failure="true"> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="ecBad.tsv"/> + </test> </tests> <help><![CDATA[Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SetGprs/SetGprs.xml --- a/build/tools/SetGprs/SetGprs.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SetGprs/SetGprs.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetGprs" name="SetGprs" version="2.0.0"> +<tool id="met4j_SetGprs" name="SetGprs" version="2.0.1"> <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetGprs#if str($colgpr) != 'nan': -cgpr "$colgpr" @@ -48,22 +48,39 @@ </outputs> <tests> <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="gpr.tsv"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> + <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> + <has_line_matching expression=".*fbc:id=.G3.*" n="1"/> + <has_line_matching expression=".*fbc:id=.G4.*" n="1"/> + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/> + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/> + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/> + <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/> + <has_line_matching expression=".*fbc:and.*" n="2"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SetIds/SetIds.xml --- a/build/tools/SetIds/SetIds.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SetIds/SetIds.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetIds" name="SetIds" version="2.0.0"> +<tool id="met4j_SetIds" name="SetIds" version="2.0.1"> <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetIds#if str($colname) != 'nan': -cnew "$colname" @@ -62,63 +62,117 @@ </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 in a SBML file from a tabulated file containing the old ids and the new ids |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SetNames/SetNames.xml --- a/build/tools/SetNames/SetNames.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SetNames/SetNames.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetNames" name="SetNames" version="2.0.0"> +<tool id="met4j_SetNames" name="SetNames" version="2.0.1"> <description>Set names to network objects in a SBML file 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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetNames#if str($colname) != 'nan': -cname "$colname" @@ -62,51 +62,94 @@ </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 in a SBML file from a tabulated file containing the object ids and the names |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SetPathways/SetPathways.xml --- a/build/tools/SetPathways/SetPathways.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SetPathways/SetPathways.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetPathways" name="SetPathways" version="2.0.0"> +<tool id="met4j_SetPathways" name="SetPathways" version="2.0.1"> <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetPathways#if str($colp) != 'nan': -cp "$colp" @@ -56,31 +56,56 @@ </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 |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SetReferences/SetReferences.xml --- a/build/tools/SetReferences/SetReferences.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SetReferences/SetReferences.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetReferences" name="SetReferences" version="2.0.0"> +<tool id="met4j_SetReferences" name="SetReferences" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetReferences#if str($colRef) != 'nan': -cr "$colRef" @@ -68,17 +68,29 @@ </outputs> <tests> <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="refs.tsv"/> + <param name="ref" value="InChi"/> + <param name="o" value="METABOLITE"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*C2H6O.*" n="3"/> + <has_line_matching expression=".*C6H8O6.*" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/SideCompoundsScan/SideCompoundsScan.xml --- a/build/tools/SideCompoundsScan/SideCompoundsScan.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/SideCompoundsScan/SideCompoundsScan.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="2.0.0"> +<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="2.0.1"> <description>Scan a network to identify side compounds.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath" $sideOnly @@ -50,23 +50,40 @@ </outputs> <tests> <test> + <param name="inputPath" value="XF_network.sbml"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_lines n="1108"/> + <has_n_columns n="4"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="noReportValue" value="true"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_lines n="6"/> + <has_n_columns n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Scan a network to identify side compounds. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/Tab2Sbml/Tab2Sbml.xml --- a/build/tools/Tab2Sbml/Tab2Sbml.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/Tab2Sbml/Tab2Sbml.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="2.0.0"> +<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="2.0.1"> <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan': -ci "$colid" @@ -76,63 +76,117 @@ </outputs> <tests> <test> + <param name="in" value="toy_model.tsv"/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*reaction .*" n="7"/> + <has_line_matching expression=".*species .*" n="8"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model_otherColumns.tsv"/> + <param name="colid" value="2"/> + <param name="colformula" value="3"/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*reaction .*" n="7"/> + <has_line_matching expression=".*species .*" n="8"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model_otherSigns.tsv"/> + <param name="i" value="->"/> + <param name="r" value="="/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*reaction .*" n="7"/> + <has_line_matching expression=".*species .*" n="8"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model.tsv"/> + <param name="rp" value="true"/> + <param name="mp" value="true"/> + <param name="e" value="_e"/> + <param name="createCompartment" value="true"/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/> + <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/> + <has_line_matching expression=".*id=.R_reac2.*" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model.tsv"/> + <param name="id" value="myModel"/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*myModel.*" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml --- a/build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/build/tools/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_TopologicalPathwayAnalysis" name="TopologicalPathwayAnalysis" version="2.0.0"> +<tool id="met4j_TopologicalPathwayAnalysis" name="TopologicalPathwayAnalysis" version="2.0.1"> <description>Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.TopologicalPathwayAnalysis -i "$inputPath" #if str($inputSide) != 'None': @@ -42,30 +42,54 @@ </outputs> <tests> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="dataPath" value="XF_network_C_NOI.txt"/> + <param name="inputSide" value="XF_network_C_Side.tab"/> + <output name="outputPath"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="3"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="dataPath" value="XF_network_C_NOI.txt"/> + <param name="inputSide" value="XF_network_C_Side.tab"/> + <param name="undirected" value="true"/> + <param name="removeIsolated" value="true"/> + <param name="out" value="true"/> + <param name="mergingStrat" value="by_id"/> + <output name="outputPath"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="3"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tests.html --- a/tests.html Mon Feb 03 15:59:46 2025 +0000 +++ b/tests.html Thu Feb 13 15:08:22 2025 +0000 |
| b |
| b"@@ -285,7 +285,7 @@\n var md = window.markdownit({\n html: true,\n });\n- target.innerHTML = 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</script>\n </body>\n </html>\n\\ No newline at end of file\n" |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/ExtractAnnotations/ExtractAnnotations.xml --- a/tools/attributes/ExtractAnnotations/ExtractAnnotations.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/ExtractAnnotations/ExtractAnnotations.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="2.0.0"> +<tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="2.0.1"> <description>Extract databases' references from SBML annotations or notes.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractAnnotations -i "$inputPath" -export "$export" @@ -34,40 +34,73 @@ </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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/ExtractPathways/ExtractPathways.xml --- a/tools/attributes/ExtractPathways/ExtractPathways.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/ExtractPathways/ExtractPathways.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractPathways" name="ExtractPathways" version="2.0.0"> +<tool id="met4j_ExtractPathways" name="ExtractPathways" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath" -p "$pathwayId" @@ -24,15 +24,25 @@ </outputs> <tests> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/> + <output ftype="sbml" name="outputPath"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*<reaction.*" n="17"/> + <has_line_matching expression=".*groups:id=.*" n="2"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/GetEntities/GetEntities.xml --- a/tools/attributes/GetEntities/GetEntities.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/GetEntities/GetEntities.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetEntities" name="GetEntities" version="2.0.0"> +<tool id="met4j_GetEntities" name="GetEntities" version="2.0.1"> <description>Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetEntities -i "$sbml" $printMetabolites @@ -30,29 +30,52 @@ </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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml --- a/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.0"> +<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml" -r "$reactionFile" @@ -34,15 +34,25 @@ </outputs> <tests> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_n_lines n="2"/> + <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> + <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml --- a/tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="2.0.0"> +<tool id="met4j_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="2.0.1"> <description>Create a tabulated file with metabolite attributes from a SBML file</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetMetaboliteAttributes -i "$sbml" -o "$outputFile" @@ -18,15 +18,25 @@ </outputs> <tests> <test> + <param name="sbml" value="toy_model.xml"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_n_lines n="9"/> + <has_n_columns n="6"/> + <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/> + <has_line_matching expression=".*C.*NC.*" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml --- a/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="2.0.0"> +<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="2.0.1"> <description>Get reactant lists from a list of reactions and a SBML file.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetReactantsFromReactions -i "$sbml" -r "$reactionFile" @@ -38,36 +38,65 @@ </outputs> <tests> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_text_matching expression="R_GLUN" n="4"/> + <has_text_matching expression="R_ACGS" n="5"/> + </assert_contents> + </output> + </test> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + <param name="printSubstrates" value="true"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_text_matching expression="R_GLUN" n="2"/> + <has_text_matching expression="R_ACGS" n="5"/> + </assert_contents> + </output> + </test> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="reactionFile" value="XF_network_R_Seed.tab"/> + <param name="printProducts" value="true"/> + <output ftype="tsv" name="outputFile"> + <assert_contents> + <has_text_matching expression="R_GLUN" n="2"/> + <has_text_matching expression="R_ACGS" n="5"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Get 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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/SetCharges/SetCharges.xml --- a/tools/attributes/SetCharges/SetCharges.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/SetCharges/SetCharges.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetCharges" name="SetCharges" version="2.0.0"> +<tool id="met4j_SetCharges" name="SetCharges" version="2.0.1"> <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetCharges#if str($colcharge) != 'nan': -cc "$colcharge" @@ -50,63 +50,117 @@ </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 metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/SetChemicalFormulas/SetChemicalFormulas.xml --- a/tools/attributes/SetChemicalFormulas/SetChemicalFormulas.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/SetChemicalFormulas/SetChemicalFormulas.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="2.0.0"> +<tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="2.0.1"> <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetChemicalFormulas#if str($colformula) != 'nan': -cf "$colformula" @@ -50,19 +50,32 @@ </outputs> <tests> <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="formula.tsv"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*CH6O6.*" n="2"/> + <has_line_matching expression=".*CH12O4.*" n="2"/> + </assert_contents> + </output> + </test> <test expect_failure="true"> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="formulaBad.tsv"/> + </test> </tests> <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/SetEcNumbers/SetEcNumbers.xml --- a/tools/attributes/SetEcNumbers/SetEcNumbers.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/SetEcNumbers/SetEcNumbers.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetEcNumbers" name="SetEcNumbers" version="2.0.0"> +<tool id="met4j_SetEcNumbers" name="SetEcNumbers" version="2.0.1"> <description>Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetEcNumbers#if str($colec) != 'nan': -cec "$colec" @@ -48,19 +48,32 @@ </outputs> <tests> <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="ec.tsv"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*1.1.1.1.*" n="2"/> + <has_line_matching expression=".*1.2.3.4.*" n="2"/> + </assert_contents> + </output> + </test> <test expect_failure="true"> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="ecBad.tsv"/> + </test> </tests> <help><![CDATA[Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/SetGprs/SetGprs.xml --- a/tools/attributes/SetGprs/SetGprs.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/SetGprs/SetGprs.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetGprs" name="SetGprs" version="2.0.0"> +<tool id="met4j_SetGprs" name="SetGprs" version="2.0.1"> <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetGprs#if str($colgpr) != 'nan': -cgpr "$colgpr" @@ -48,22 +48,39 @@ </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 |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/SetIds/SetIds.xml --- a/tools/attributes/SetIds/SetIds.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/SetIds/SetIds.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetIds" name="SetIds" version="2.0.0"> +<tool id="met4j_SetIds" name="SetIds" version="2.0.1"> <description>Set new ids to network objects in a SBML file 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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetIds#if str($colname) != 'nan': -cnew "$colname" @@ -62,63 +62,117 @@ </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 in a SBML file from a tabulated file containing the old ids and the new ids |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/SetNames/SetNames.xml --- a/tools/attributes/SetNames/SetNames.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/SetNames/SetNames.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetNames" name="SetNames" version="2.0.0"> +<tool id="met4j_SetNames" name="SetNames" version="2.0.1"> <description>Set names to network objects in a SBML file 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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetNames#if str($colname) != 'nan': -cname "$colname" @@ -62,51 +62,94 @@ </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 in a SBML file from a tabulated file containing the object ids and the names |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/SetPathways/SetPathways.xml --- a/tools/attributes/SetPathways/SetPathways.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/SetPathways/SetPathways.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetPathways" name="SetPathways" version="2.0.0"> +<tool id="met4j_SetPathways" name="SetPathways" version="2.0.1"> <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetPathways#if str($colp) != 'nan': -cp "$colp" @@ -56,31 +56,56 @@ </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 |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/attributes/SetReferences/SetReferences.xml --- a/tools/attributes/SetReferences/SetReferences.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/attributes/SetReferences/SetReferences.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetReferences" name="SetReferences" version="2.0.0"> +<tool id="met4j_SetReferences" name="SetReferences" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetReferences#if str($colRef) != 'nan': -cr "$colRef" @@ -68,17 +68,29 @@ </outputs> <tests> <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="refs.tsv"/> + <param name="ref" value="InChi"/> + <param name="o" value="METABOLITE"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*C2H6O.*" n="3"/> + <has_line_matching expression=".*C6H8O6.*" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/bigg/GetBiggModelProteome/GetBiggModelProteome.xml --- a/tools/bigg/GetBiggModelProteome/GetBiggModelProteome.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/bigg/GetBiggModelProteome/GetBiggModelProteome.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="2.0.0"> +<tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="2.0.1"> <description>Get proteome in fasta format of a model present in the BIGG database</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetBiggModelProteome -m "$modelId" -o "$outputFile" @@ -22,12 +22,19 @@ </outputs> <tests> <test maxseconds="120"> + <param name="modelId" value="e_coli_core"/> + <output ftype="fasta" name="outputFile"> + <assert_contents> + <has_line_matching expression=".*name=.*" n="136"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/convert/FbcToNotes/FbcToNotes.xml --- a/tools/convert/FbcToNotes/FbcToNotes.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/convert/FbcToNotes/FbcToNotes.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_FbcToNotes" name="FbcToNotes" version="2.0.0"> +<tool id="met4j_FbcToNotes" name="FbcToNotes" version="2.0.1"> <description>Convert FBC package annotations to sbml html notes</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath" -o "$outputPath" @@ -18,13 +18,21 @@ </outputs> <tests> <test> + <param name="inputPath" value="ECOL.xml"/> + <output ftype="sbml" name="outputPath"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Convert FBC package annotations to sbml html notes (see https://www.degruyter.com/document/doi/10.1515/jib-2017-0082/html)]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/convert/Kegg2Sbml/Kegg2Sbml.xml --- a/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="2.0.0"> +<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="2.0.1"> <description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org): -org "$org" |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/convert/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml --- a/tools/convert/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/convert/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="2.0.0"> +<tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="2.0.1"> <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CarbonSkeletonNet -i "$inputPath" -g "$inputAAM" @@ -46,90 +46,168 @@ </outputs> <tests> <test> + <param name="inputPath" value="Human-GEM_pathways.xml"/> + <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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="format" value="matrix"/> + <output name="output"> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <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 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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml --- a/tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.0"> +<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.1"> <description>Advanced creation of a compound graph representation of a SBML file content</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CompoundGraph -i "$inputPath" #if str($inputSide) != 'None': @@ -54,31 +54,56 @@ </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. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/convert/Sbml2Graph/Sbml2Graph.xml --- a/tools/convert/Sbml2Graph/Sbml2Graph.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/convert/Sbml2Graph/Sbml2Graph.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="2.0.0"> +<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="2.0.1"> <description>Create a graph representation of a SBML file content, and export it in graph file format.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" $bipartite @@ -34,38 +34,69 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="format" value="gml"/> + <output name="output"> + <assert_contents> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <assert_contents> + <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"/> + <param name="format" value="gml"/> + <output name="output"> + <assert_contents> + <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. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/convert/Sbml2PathwayNet/Sbml2PathwayNet.xml --- a/tools/convert/Sbml2PathwayNet/Sbml2PathwayNet.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/convert/Sbml2PathwayNet/Sbml2PathwayNet.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2PathwayNet" name="Sbml2PathwayNet" version="2.0.0"> +<tool id="met4j_Sbml2PathwayNet" name="Sbml2PathwayNet" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2PathwayNet -i "$inputPath" #if str($inputSide) != 'None': |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/convert/Sbml2Tab/Sbml2Tab.xml --- a/tools/convert/Sbml2Tab/Sbml2Tab.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/convert/Sbml2Tab/Sbml2Tab.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.0"> +<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.1"> <description>Create a tabulated file listing reaction attributes from a SBML file</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): -irr "$i" @@ -34,28 +34,50 @@ </outputs> <tests> <test> + <param name="in" value="toy_model.xml"/> + <output ftype="tsv" name="out"> + <assert_contents> + <has_n_lines n="8"/> + <has_n_columns n="9"/> + <has_text text="2.0 E[c] --> D[c]"/> + <has_text text="A[c] <==> B[c]"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model.xml"/> + <param name="i" value="->"/> + <param name="r" value="="/> + <output ftype="tsv" name="out"> + <assert_contents> + <has_n_lines n="8"/> + <has_n_columns n="9"/> + <has_text text="2.0 E[c] -> D[c]"/> + <has_text text="A[c] = B[c]"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/convert/SbmlWizard/SbmlWizard.xml --- a/tools/convert/SbmlWizard/SbmlWizard.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/convert/SbmlWizard/SbmlWizard.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.0"> +<tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.1"> <description>General SBML model processing</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath" #if str($inputSide) != 'None': @@ -56,30 +56,54 @@ </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> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/convert/Tab2Sbml/Tab2Sbml.xml --- a/tools/convert/Tab2Sbml/Tab2Sbml.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/convert/Tab2Sbml/Tab2Sbml.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="2.0.0"> +<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="2.0.1"> <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan': -ci "$colid" @@ -76,63 +76,117 @@ </outputs> <tests> <test> + <param name="in" value="toy_model.tsv"/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*reaction .*" n="7"/> + <has_line_matching expression=".*species .*" n="8"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model_otherColumns.tsv"/> + <param name="colid" value="2"/> + <param name="colformula" value="3"/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*reaction .*" n="7"/> + <has_line_matching expression=".*species .*" n="8"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model_otherSigns.tsv"/> + <param name="i" value="->"/> + <param name="r" value="="/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*reaction .*" n="7"/> + <has_line_matching expression=".*species .*" n="8"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model.tsv"/> + <param name="rp" value="true"/> + <param name="mp" value="true"/> + <param name="e" value="_e"/> + <param name="createCompartment" value="true"/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/> + <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/> + <has_line_matching expression=".*id=.R_reac2.*" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="in" value="toy_model.tsv"/> + <param name="id" value="myModel"/> + <output ftype="sbml" name="sbml"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*myModel.*" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/mapping/NameMatcher/NameMatcher.xml --- a/tools/mapping/NameMatcher/NameMatcher.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/mapping/NameMatcher/NameMatcher.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_NameMatcher" name="NameMatcher" version="2.0.0"> +<tool id="met4j_NameMatcher" name="NameMatcher" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.NameMatcher#if str($n): -nMatch "$n" @@ -60,6 +60,7 @@ </outputs> <tests/> <help><![CDATA[Metabolic models and Metabolomics Data often refer compounds only by using their common names, which vary greatly according to the source, thus impeding interoperability between models, databases and experimental data. This requires a tedious step of manual mapping. Fuzzy matching is a range of methods which can potentially helps fasten this process, by allowing the search for near-similar names. Fuzzy matching is primarily designed for common language search engines and is frequently based on edit distance, i.e. the number of edits to transform a character string into another, effectively managing typo, case and special character variations, and allowing auto-completion. However, edit-distance based search fall short when mapping chemical names: As an example, alpha-D-Glucose et Glucose would require more edits than between Fructose and Glucose. + 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.]]></help> <citations/> </tool> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml --- a/tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="2.0.0"> +<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="2.0.1"> <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != 'nan': -th "$th" @@ -32,39 +32,62 @@ </outputs> <tests> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="input" value="XF_network_C_NOI.txt"/> + <output name="outputFile"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="3"/> + </assert_contents> + </output> + </test> <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="input" value="XF_network_C_NOI.txt"/> + <param name="corr" value="HolmBonferroni"/> + <param name="th" value="0.005"/> + <output name="outputFile"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="2"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test. The fisher exact test computes the probability p to randomly get the given set of values. This version computes the probability to get at least the given overlap between the given set and the given modality : Sum the hypergeometric probability with increasing target/query intersection cardinality. + The hypergeometric probability is computed from the following contingency table entries. (values in cells correspond to the marginal totals of each intersection groups) Query !Query Target a b !Target c d + The probability of obtaining the set of value is computed as following: p = ((a+b)!(c+d)!(a+c)!(b+d)!)/(a!b!c!d!(a+b+c+d)!) + The obtained p-value is then adjusted for multiple testing using one of the following methods: - Bonferroni: adjusted p-value = p*n - Benjamini-Hochberg: adjusted p-value = p*n/k |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml --- a/tools/networkAnalysis/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="2.0.0"> +<tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.BipartiteDistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml --- a/tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="2.0.0"> +<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="2.0.1"> <description>Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type): -f "$type" @@ -68,7 +68,7 @@ <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search.]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btg217</citation> + <citation type="doi">10.1093/bioinformatics/btu760</citation> <citation type="doi">10.1093/bioinformatics/bti116</citation> - <citation type="doi">10.1093/bioinformatics/btu760</citation> </citations> </tool> |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/ChokePoint/ChokePoint.xml --- a/tools/networkAnalysis/ChokePoint/ChokePoint.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/ChokePoint/ChokePoint.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ChokePoint" name="ChokePoint" version="2.0.0"> +<tool id="met4j_ChokePoint" name="ChokePoint" version="2.0.1"> <description>Compute the Choke points of a metabolic network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath" -o "$outputPath" @@ -18,15 +18,25 @@ </outputs> <tests> <test> + <param name="inputPath" value="XF_network.sbml"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_lines n="695"/> + <has_n_columns n="3"/> + <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e <==> M_ade_p" n="1"/> + <has_line_matching expression="R_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --> M_ac_c \+ M_gam6p_c" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Compute the Choke points of a metabolic network. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml --- a/tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="2.0.0"> +<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="2.0.1"> <description>Provides tabulated compound graph edge list, with one column with target's degree.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DegreeWeighting#if str($pow): -pow "$pow" |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml --- a/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="2.0.0"> +<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="2.0.1"> <description>Create a compound to compound distance matrix.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -34,30 +34,54 @@ </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 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml --- a/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="2.0.0"> +<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath" -s "$sourcePath" @@ -54,17 +54,29 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="sourcePath" value="seeds.txt"/> + <param name="targetPath" value="targets.txt"/> + <param name="sideCompoundFile" value="sc.txt"/> + <param name="format" value="gml"/> + <output ftype="txt" name="output"> + <assert_contents> + <has_line_matching expression=".*node.*" n="5"/> + <has_line_matching expression=".*edge.*" n="4"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml --- a/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="2.0.0"> +<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="2.0.1"> <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath" -s "$sourcePath" @@ -56,29 +56,41 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="sourcePath" value="seeds.txt"/> + <param name="targetPath" value="targets.txt"/> + <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 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.]]></help> <citations> + <citation type="doi">10.1093/nar/gki437</citation> + <citation type="doi">10.1093/bioinformatics/btg217</citation> <citation type="doi">10.1093/bib/bbv115</citation> <citation type="doi">10.1016/j.biosystems.2011.05.004</citation> + <citation type="doi">10.1093/bioinformatics/bti116</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 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml --- a/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="2.0.0"> +<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath" -s "$sourcePath" @@ -54,17 +54,29 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="sourcePath" value="seeds.txt"/> + <param name="targetPath" value="targets.txt"/> + <param name="sideCompoundFile" value="sides.txt"/> + <param name="format" value="gml"/> + <output ftype="txt" name="output"> + <assert_contents> + <has_line_matching expression=".*node.*" n="3"/> + <has_line_matching expression=".*edge.*" n="2"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/LoadPoint/LoadPoint.xml --- a/tools/networkAnalysis/LoadPoint/LoadPoint.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/LoadPoint/LoadPoint.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_LoadPoint" name="LoadPoint" version="2.0.0"> +<tool id="met4j_LoadPoint" name="LoadPoint" version="2.0.1"> <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -30,13 +30,21 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="8"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/MetaboRank/MetaboRank.xml --- a/tools/networkAnalysis/MetaboRank/MetaboRank.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/MetaboRank/MetaboRank.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_MetaboRank" name="MetaboRank" version="2.0.0"> +<tool id="met4j_MetaboRank" name="MetaboRank" version="2.0.1"> <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath" -s "$seedsFilePath" @@ -44,15 +44,25 @@ </outputs> <tests> <test> + <param name="sbmlFilePath" value="XF_network.sbml"/> + <param name="seedsFilePath" value="XF_network_C_Seed.tab"/> + <param name="inputSide" value="XF_network_C_Side.tab"/> + <output name="output"> + <assert_contents> + <has_n_lines n="1100"/> + <has_n_columns n="11"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/NetworkSummary/NetworkSummary.xml --- a/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_NetworkSummary" name="NetworkSummary" version="2.0.0"> +<tool id="met4j_NetworkSummary" name="NetworkSummary" version="2.0.1"> <description>Create a report summarizing several graph measures characterising the structure of a metabolic network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -26,12 +26,19 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <output name="outputPath"> + <assert_contents> + <has_n_lines min="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a report summarizing several graph measures characterising the structure of a metabolic network. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml --- a/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="2.0.0"> +<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="2.0.1"> <description>Perform a network expansion from a set of compound targets to create a precursor network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" -t "$targetsFilePath" @@ -38,15 +38,25 @@ </outputs> <tests> <test> + <param name="sbmlFilePath" value="toy_model.xml"/> + <param name="targetsFilePath" value="targets.txt"/> + <param name="format" value="gml"/> + <output ftype="txt" name="output"> + <assert_contents> + <has_line_matching expression=".*node.*" n="13"/> + <has_line_matching expression=".*edge.*" n="15"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml --- a/tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="2.0.0"> +<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="2.0.1"> <description>Create a reaction to reaction distance matrix.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -38,91 +38,172 @@ </outputs> <tests> <test> + <param name="inputPath" value="toy_model.xml"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="8"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/> + <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="undirected" value="true"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="8"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/> + <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="undirected" value="true"/> + <param name="sideCompoundFile" value="sides.txt"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="8"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/> + <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/> + <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/> + <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="undirected" value="true"/> + <param name="rExclude" value="rexclude.txt"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="6"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/> + <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/> + <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/> + <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="undirected" value="true"/> + <param name="sideCompoundFile" value="sides.txt"/> + <param name="rExclude" value="rexclude.txt"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="6"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/> + <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/> + <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="sideCompoundFile" value="sides.txt"/> + <param name="rExclude" value="rexclude.txt"/> + <output ftype="csv" name="outputPath"> + <assert_contents> + <has_n_lines n="6"/> + <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> + <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/> + <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/> + <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/> + <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a reaction to reaction distance matrix. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml --- a/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="2.0.0"> +<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="2.0.1"> <description>Perform a network expansion from a set of compound seeds to create a scope network</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath" -s "$seedsFilePath" @@ -42,16 +42,27 @@ </outputs> <tests> <test> + <param name="sbmlFilePath" value="toy_model.xml"/> + <param name="seedsFilePath" value="seeds.txt"/> + <param name="sideCompoundFile" value="sides.txt"/> + <param name="format" value="gml"/> + <output ftype="txt" name="output"> + <assert_contents> + <has_line_matching expression=".*node.*" n="9"/> + <has_line_matching expression=".*edge.*" n="11"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml --- a/tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="2.0.0"> +<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="2.0.1"> <description>Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath" #if str($inputSide) != 'None': @@ -44,41 +44,75 @@ </outputs> <tests> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="source" value="true"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_columns n="1"/> + <has_n_lines n="109"/> + <has_line_matching expression="M_\S+_\w" n="109"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="sink" value="true"/> + <param name="useInternal" value="true"/> + <param name="comp" value="e"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_columns n="1"/> + <has_n_lines n="5"/> + <has_line_matching expression="^M_\S+_\w" n="5"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="sink" value="true"/> + <param name="useBorensteinAlg" value="true"/> + <param name="comp" value="e"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_columns n="1"/> + <has_n_lines n="26"/> + <has_line_matching expression="^M_\S+_\w" n="26"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml --- a/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="2.0.0"> +<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="2.0.1"> <description>Scan a network to identify side compounds.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath" $sideOnly @@ -50,23 +50,40 @@ </outputs> <tests> <test> + <param name="inputPath" value="XF_network.sbml"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_lines n="1108"/> + <has_n_columns n="4"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="noReportValue" value="true"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_lines n="6"/> + <has_n_columns n="1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Scan a network to identify side compounds. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/networkAnalysis/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml --- a/tools/networkAnalysis/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/networkAnalysis/TopologicalPathwayAnalysis/TopologicalPathwayAnalysis.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_TopologicalPathwayAnalysis" name="TopologicalPathwayAnalysis" version="2.0.0"> +<tool id="met4j_TopologicalPathwayAnalysis" name="TopologicalPathwayAnalysis" version="2.0.1"> <description>Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.TopologicalPathwayAnalysis -i "$inputPath" #if str($inputSide) != 'None': @@ -42,30 +42,54 @@ </outputs> <tests> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="dataPath" value="XF_network_C_NOI.txt"/> + <param name="inputSide" value="XF_network_C_Side.tab"/> + <output name="outputPath"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="3"/> + </assert_contents> + </output> + </test> <test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="dataPath" value="XF_network_C_NOI.txt"/> + <param name="inputSide" value="XF_network_C_Side.tab"/> + <param name="undirected" value="true"/> + <param name="removeIsolated" value="true"/> + <param name="out" value="true"/> + <param name="mergingStrat" value="by_id"/> + <output name="outputPath"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="3"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/reconstruction/CreateMetaNetwork/CreateMetaNetwork.xml --- a/tools/reconstruction/CreateMetaNetwork/CreateMetaNetwork.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/reconstruction/CreateMetaNetwork/CreateMetaNetwork.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.0"> +<tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.1"> <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:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath" -n2 "$sbml2FilePath" @@ -60,18 +60,31 @@ </outputs> <tests> <test> + <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/> + <param name="sbml2FilePath" value="ECOL.xml"/> + <param name="external1" value="s"/> + <param name="external2" value="e"/> + <param name="n1prefix" value="hsa"/> + <param name="n2prefix" value="eco"/> + <param name="mergingCriterion" value="by_metanetx"/> + <output ftype="sbml" name="outputPath"> + <assert_contents> + <has_text text="</sbml>"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format. |
| b |
| diff -r 6a112eaf8f38 -r 40c15b7467f1 tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml --- a/tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml Mon Feb 03 15:59:46 2025 +0000 +++ b/tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml Thu Feb 13 15:08:22 2025 +0000 |
| [ |
| @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="2.0.0"> +<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="2.0.1"> <description>Check balance of all the reactions in a SBML.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.SbmlCheckBalance -i "$sbml" -out "$out" |