Mercurial > repos > metexplore > met4j_sbml2tab
changeset 0:897bc123f6c5 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
| author | metexplore |
|---|---|
| date | Thu, 13 Mar 2025 15:49:53 +0000 |
| parents | |
| children | be58dd7c74ee |
| files | Sbml2Tab.xml macros.xml test-data/toy_model.xml |
| diffstat | 3 files changed, 202 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Sbml2Tab.xml Thu Mar 13 15:49:53 2025 +0000 @@ -0,0 +1,63 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="@TOOL_VERSION@"> + <description>Create a tabulated file listing reaction attributes from a SBML file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[met4j fr.inrae.toulouse.metexplore.met4j_toolbox.convert.Sbml2Tab#if str($i): + -irr "$i" +#end if +#if str($r): + -rev "$r" +#end if + -i "$in" + -o "$out" +]]></command> + <inputs> + <param argument="-irr" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-rev" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-i" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/> + </inputs> + <outputs> + <data format="tsv" name="out"/> + </outputs> + <tests> + <test> + <param name="in" value="toy_model.xml"/> + <output ftype="tsv" name="out"> + <assert_contents> + <has_n_lines n="8"/> + <has_n_columns n="9"/> + <has_text text="2.0 E[c] --> D[c]"/> + <has_text text="A[c] <==> B[c]"/> + </assert_contents> + </output> + </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 +@ATTRIBUTION@]]></help> + <citations/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 13 15:49:53 2025 +0000 @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.0.1">met4j</requirement> + <yield/> + </requirements> + </xml> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + </xml> + <token name="@TOOL_VERSION@">2.0.1</token> + <token name="@ATTRIBUTION@"><![CDATA[ +**Attribution** + +This Galaxy tool relies on the met4j toolkit which is dedicated to the structural analysis of metabolic networks (https://forgemia.inra.fr/metexplore/met4j) + ]]></token> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toy_model.xml Thu Mar 13 15:49:53 2025 +0000 @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding='UTF-8' ?> +<sbml fbc:required="false" groups:required="false" level="3" version="1" + xmlns="http://www.sbml.org/sbml/level3/version1/core" + xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" + xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" name="toy model"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="false" id="c" name="Cytosol"/> + <compartment constant="false" id="e" name="Extracellular"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> + <notes> + <body xmlns="http://www.w3.org/1999/xhtml"> + <p>SMILES: C[C@@H](C(=O)O)NC</p> + </body> + </notes> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#A_ext"> + <bqbiol:is> + <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + + </species> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> + <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> + <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> + <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> + <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> + </listOfParameters> + <listOfReactions> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="A" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="B" stoichiometry="1.0"/> + <speciesReference constant="true" species="C" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.5"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="E" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> + <listOfReactants> + <speciesReference constant="true" species="E" stoichiometry="2.0"/> + </listOfReactants> + <listOfProducts> + <speciesReference constant="true" species="D" stoichiometry="1.0"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml> \ No newline at end of file