| Previous changeset 5:80c32f0cb716 (2023-05-30) Next changeset 7:8dc4d3964ab5 (2023-09-04) |
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Commit message:
planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 87a863d4074543870caef1116b8e9be58005dcdd |
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modified:
get_sbml_model.xml |
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added:
test-data/e_coli_core.xml |
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| diff -r 80c32f0cb716 -r 9b5947d48192 get_sbml_model.xml --- a/get_sbml_model.xml Tue May 30 21:03:04 2023 +0000 +++ b/get_sbml_model.xml Mon Aug 28 14:24:48 2023 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT">\n+<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.4" profile="21.09" license="MIT">\n <description>Get an SBML model (BiGG)</description>\n <requirements>\n <requirement type="package" version="7.81.0">curl</requirement>\n@@ -7,87 +7,117 @@\n <requirement type="package" version="2.29">requests</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n- curl -o - \'http://bigg.ucsd.edu/static/models/$(input).xml.gz\'\n- | gunzip > \'$model\';\n+ #if str($cond_src.from_src) == \'from_bigg\'\n+ curl -o - \'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz\' | gunzip > \'$model\' &&\n+ #else\n+ cp \'${cond_src.input_file}\' \'$model\' &&\n+ #end if\n python \'$__tool_directory__/\'get_infos.py\n \'$model\'\n- --hostid \'$input\'\n+ --hostid \'${cond_src.hostid}\'\n --comp \'$compartments\'\n --biomass \'$biomass\'\n --taxid \'$taxid\'\n ]]></command>\n <inputs>\n- <param name="input" type="select" label="Strain">\n- <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>\n- <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>\n- <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option>\n- <option value="iCN900">Clostridioides difficile 630 (iCN900)</option>\n- <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option>\n- <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option>\n- <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>\n- <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>\n- <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>\n- <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>\n- <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>\n- <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>\n- <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>\n- <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>\n- <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>\n- <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>\n- <option value="Recon3D">Homo sapiens (Recon3D)</option>\n- <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>\n- <option value="RECON1">Homo sapiens (RECON1)</option>\n- <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>\n- <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>\n- <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>\n- <option value="iMM1415">Mus musculus (iMM1415)</option>\n- <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>\n- <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>\n- <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>\n- <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>\n- <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>\n- <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>\n- <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option>\n- <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option>\n- <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option>\n- '..b'ption value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>\n+ <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>\n+ <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>\n+ <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>\n+ <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>\n+ <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>\n+ <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>\n+ <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>\n+ <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>\n+ <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>\n+ <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>\n+ <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>\n+ <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>\n+ </param>\n+ </when>\n+ </conditional>\n </inputs>\n <outputs>\n- <data name="model" format="sbml" label="${input}" />\n- <data name="taxid" format="tsv" label="${input} (taxon id)" />\n- <data name="compartments" format="tsv" label="${input} (compartments)" />\n- <data name="biomass" format="tsv" label="${input} (biomass reactions)" />\n+ <data name="model" format="sbml" label="${cond_src.hostid}" />\n+ <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" />\n+ <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" />\n+ <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />\n </outputs>\n <tests>\n <test>\n- <!-- test 1: check if identical outputs are produced with iML1515 model input -->\n- <param name="input" value="iML1515" />\n- <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>\n- <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e"/>\n- <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>\n- <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>\n+ <conditional name="cond_src">\n+ <param name="from_src" value="from_bigg" />\n+ <param name="hostid" value="iML1515" />\n+ </conditional>\n+ <output name="model" md5="9bf81d20cab5476700697ded95b716d1" />\n+ <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />\n+ <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />\n+ <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />\n </test>\n+ <test>\n+ <conditional name="cond_src">\n+ <param name="from_src" value="from_history" />\n+ <param name="hostid" value="e_coli_core" />\n+ <param name="input_file" value="e_coli_core.xml" />\n+ </conditional>\n+ <output name="model" md5="4574760460afe9e1b3388dc15f354706" />\n+ <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />\n+ <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />\n+ <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />\n+ </test>\n </tests>\n <help><![CDATA[\n Pick SBML Model\n =================\n \n-Download the selected SBML model fromg BiGG database.\n+Download the selected SBML model fromg BiGG database or get statistics from local SBML model.\n ]]></help>\n <creator>\n <organization name="BioRetroSynth" url="https://github.com/brsynth"/>\n' |
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| diff -r 80c32f0cb716 -r 9b5947d48192 test-data/e_coli_core.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_core.xml Mon Aug 28 14:24:48 2023 +0000 |
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| b'@@ -0,0 +1,9898 @@\n+<?xml version=\'1.0\' encoding=\'UTF-8\'?>\n+<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1" sboTerm="SBO:0000624" fbc:required="false">\n+ <model fbc:strict="true" id="e_coli_core">\n+ <listOfUnitDefinitions>\n+ <unitDefinition id="mmol_per_gDW_per_hr">\n+ <listOfUnits>\n+ <unit kind="mole" scale="-3" multiplier="1" exponent="1"/>\n+ <unit kind="gram" scale="0" multiplier="1" exponent="-1"/>\n+ <unit kind="second" scale="0" multiplier="3600" exponent="-1"/>\n+ </listOfUnits>\n+ </unitDefinition>\n+ </listOfUnitDefinitions>\n+ <fbc:listOfObjectives fbc:activeObjective="obj">\n+ <fbc:objective fbc:id="obj" fbc:type="maximize">\n+ <fbc:listOfFluxObjectives>\n+ <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ecoli_core_w_GAM" fbc:coefficient="1"/>\n+ </fbc:listOfFluxObjectives>\n+ </fbc:objective>\n+ </fbc:listOfObjectives>\n+ <listOfParameters>\n+ <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>\n+ <parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>\n+ <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>\n+ <parameter id="R_ATPM_lower_bound" value="8.39" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>\n+ <parameter id="R_EX_glc__D_e_lower_bound" value="-10" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>\n+ </listOfParameters>\n+ <listOfCompartments>\n+ <compartment id="e" name="extracellular space" constant="true"/>\n+ <compartment id="c" name="cytosol" constant="true"/>\n+ </listOfCompartments>\n+ <listOfSpecies>\n+ <species id="M_glc__D_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="D-Glucose" metaid="M_glc__D_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C6H12O6">\n+ <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n+ <rdf:Description rdf:about="#M_glc__D_e">\n+ <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/glc__D"/>\n+ <rdf:li rdf:resource="http://identifiers.org/biocyc/META:Glucopyranose"/>\n+ <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:12965"/>\n+ <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:20999"/>\n+ <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:4167"/>\n+ <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17634"/>\n+ <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00122"/>\n+ <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB06564"/>\n+ <rdf:li rdf:resource="http://identifiers.org/inchi_key/WQZGKKKJIJFFOK-GASJEMHNSA-N"/>\n+ <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00031"/>\n+ <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00009"/>\n+ <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM41"/>\n+ <rdf:li rdf:resource="http://identifiers.org/sabiork/1406"/>\n+ <rdf:li rdf:resource="http://identifiers.org/sabiork/1407"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd26821"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00027"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </sbml:annotation>\n+ </species>\n+ '..b'ource="http://identifiers.org/biocyc/META:PYRUVDEH-RXN"/>\n+ <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1"/>\n+ <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.4"/>\n+ <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.51"/>\n+ <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.4.1"/>\n+ <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.12"/>\n+ <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00209"/>\n+ <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102425"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373177"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71397"/>\n+ <rdf:li rdf:resource="http://identifiers.org/rhea/28043"/>\n+ <rdf:li rdf:resource="http://identifiers.org/rhea/28045"/>\n+ <rdf:li rdf:resource="http://identifiers.org/rhea/28044"/>\n+ <rdf:li rdf:resource="http://identifiers.org/rhea/28042"/>\n+ <rdf:li rdf:resource="http://identifiers.org/sabiork/523"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00154"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </sbml:annotation>\n+ <listOfReactants>\n+ <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>\n+ </listOfProducts>\n+ <fbc:geneProductAssociation>\n+ <fbc:and>\n+ <fbc:geneProductRef fbc:geneProduct="G_b0114"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_b0115"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_b0116"/>\n+ </fbc:and>\n+ </fbc:geneProductAssociation>\n+ </reaction>\n+ </listOfReactions>\n+ </model>\n+</sbml>\n' |