Mercurial > repos > tduigou > rpthermo
changeset 0:44e54b56328d draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Wed, 24 Nov 2021 09:48:18 +0000 |
| parents | |
| children | 21a900eee812 |
| files | rpthermo.xml test-data/rp_013_0001.xml test-data/rp_013_0001_with_thermo.xml |
| diffstat | 3 files changed, 983 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpthermo.xml Wed Nov 24 09:48:18 2021 +0000 @@ -0,0 +1,103 @@ +<tool id="rpThermo" name="Thermodynamics" version="5.9.2"> + <description>Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML</description> + <requirements> + <requirement type="package" version="5.9.2">rptools</requirement> + </requirements> + <stdio> + <regex match="WARNING:" level="warning" /> + <regex match="ERROR:" level="fatal" /> + <regex match="ERROR:root:ChemAxon" level="warning" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + python -m rptools.rpthermo + '$input' + '$pathway_with_thermo' + --ph '$adv.ph' + --ionic_strength '$adv.ionic_strength' + --pMg '$adv.pMg' + --temp_k '$adv.temp_k' + ]]></command> + <inputs> + <param name="input" type="data" format="xml" label="Input File" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="ph" type="float" value="7.5" label="Compartment PH of the pathway" /> + <param name="ionic_strength" type="float" value="200.0" label="Compartment ionic strength of the pathway" /> + <param name="pMg" type="float" value="10.0" label="Compartment pMg of the pathway" /> + <param name="temp_k" type="float" value="298.15" label="Compartment temperature in Kelvin" /> + </section> + </inputs> + <outputs> + <data name="pathway_with_thermo" format="xml" label="${tool.name} - ${input.name}" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with default parameters --> + <param name="input" value="rp_013_0001.xml" /> + <param name="model" value="e_coli_iML1515.sbml" /> + <output name="pathway_with_thermo" file="rp_013_0001_with_thermo.xml" ftype="xml" compare="diff" sort="true"/> + </test> + </tests> + <help><![CDATA[ +Thermodynamics +=============== +Calculate the formation energy of chemical species either using an internal database or estimate it by decomposing them using the `component contribution <https://gitlab.com/elad.noor/component-contribution>`_ method. Thereafter this tool predicts the Gibbs free energy of reactions and of the whole heterologous pathway by combining the formation energy of each individual compound. + +.. image:: https://raw.githubusercontent.com/Galaxy-SynBioCAD/rpThermo/standalone/galaxy/img/rpThermo.png + :width: 80 % + :align: center + + +| + + +Above is an illustration of the Gibbs free energy calculation using the component contribution package. The color-coded arrows from red (best) to blue (worst) show the best and worst-performing reactions. + +Required: + +* **input**\ : (string) Path to the input file +* **output**\ : (string) Path to the output file + +Advanced Options: + +* **--ph**\ :(float) Compartment PH of the pathway +* **--ionic_strength**\ :(float) Compartment ionic strength of the pathway +* **--pMg**\ :(float) Compartment pMg of the pathway +* **--temp_k**\ :(float) Compartment temperature in Kelvin + +Project Links +--------------------- + +* `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpthermo>`_ + +Version +---------- + +v5.9.2 + +Authors +------- + +* **Melchior du Lac** + +Acknowledgments +--------------- + +* Thomas Duigou +* Joan Hérisson + + ]]></help> + <citations> + <citation type="bibtex"> +@article{noor2013consistent, + title={Consistent estimation of Gibbs energy using component contributions}, + author={Noor, Elad and Haraldsd{\'o}ttir, Hulda S and Milo, Ron and Fleming, Ronan MT}, + journal={PLoS Comput Biol}, + volume={9}, + number={7}, + pages={e1003098}, + year={2013}, + publisher={Public Library of Science} +} + </citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rp_013_0001.xml Wed Nov 24 09:48:18 2021 +0000 @@ -0,0 +1,397 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false"> + <model metaid="_2db93def850b5b412e9c6bfb2f3ae31a33b90fb03a3777278e0e69de0adbd9b8" id="RP_model_013_0001" name="013_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true"> + <listOfCompartments> + <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description 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constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC__10000" fbc:upperFluxBound="BRS_FBC_10000"> + <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="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.13.7"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1[H].[H+].O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]>>[H]Oc1c([H])c([H])c([H])c([H])c1O[H].[H]O[H].N=C(O)c1ccc[n+](C2OC(COP(=O)(O)OP(=O)(O)OCC3OC(n4cnc5c(N)ncnc54)C(OP(=O)(O)O)C3O)C(O)C2O)c1"/> + <brsynth:rp2_transfo_id value="TRS_0_1_3"/> + <brsynth:rule_id value="RR-02-217503934671e143-16-F"/> + <brsynth:tmpl_rxn_id value="MNXR106703"/> + <brsynth:rule_score value="0.5683242688496836"/> + <brsynth:idx_in_path value="2"/> + <brsynth:selenzy/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="MNXM4" stoichiometry="1" constant="true"/> + <speciesReference species="CMPD_0000000003" stoichiometry="2" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="MNXM1" stoichiometry="1" constant="true"/> + <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC__10000" fbc:upperFluxBound="BRS_FBC_10000"> + <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="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.61"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H+].[H]OC(=O)c1c([H])c([H])c(O[H])c([H])c1[H]>>[H]Oc1c([H])c([H])c([H])c([H])c1[H].O=C=O"/> + <brsynth:rp2_transfo_id value="TRS_0_2_60"/> + <brsynth:rule_id value="RR-02-d3b162f199b260fc-16-F"/> + <brsynth:tmpl_rxn_id value="MNXR106877"/> + <brsynth:rule_score value="0.7023718970192103"/> + <brsynth:idx_in_path value="1"/> + <brsynth:selenzy/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="MNXM188" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM4" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM6" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM1" stoichiometry="3" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="CMPD_0000000004" stoichiometry="1" constant="true"/> + <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM13" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM15" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM5" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + </listOfReactions> + <groups:listOfGroups> + <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:global_score value="-1"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="rxn_1"/> + <groups:member groups:idRef="rxn_2"/> + <groups:member groups:idRef="rxn_3"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="CMPD_0000000004"/> + <groups:member groups:idRef="CMPD_0000000003"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="TARGET_0000000001"/> + <groups:member groups:idRef="MNXM4"/> + <groups:member groups:idRef="MNXM164"/> + <groups:member groups:idRef="CMPD_0000000004"/> + <groups:member groups:idRef="CMPD_0000000003"/> + <groups:member groups:idRef="MNXM6"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM5"/> + <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM2"/> + <groups:member groups:idRef="MNXM1"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM2"/> + <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM4"/> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM164"/> + <groups:member groups:idRef="MNXM5"/> + <groups:member groups:idRef="MNXM6"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rp_013_0001_with_thermo.xml Wed Nov 24 09:48:18 2021 +0000 @@ -0,0 +1,483 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false"> + <model metaid="_2db93def850b5b412e9c6bfb2f3ae31a33b90fb03a3777278e0e69de0adbd9b8" id="RP_model_013_0001" name="013_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true"> + <listOfCompartments> + <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true"> + <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="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/> + <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/> + <rdf:li rdf:resource="http://identifiers.org/seed/c"/> + <rdf:li rdf:resource="http://identifiers.org/seed/c0"/> + <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/> + <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </compartment> + </listOfCompartments> + <listOfSpecies> + <species metaid="_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb" id="MNXM6" name="MNXM6" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <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="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]"/> + <brsynth:inchi value="InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)"/> + <brsynth:inchikey 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</annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM2"/> + <groups:member groups:idRef="MNXM5"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM4"/> + <groups:member groups:idRef="MNXM6"/> + <groups:member groups:idRef="MNXM2"/> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM164"/> + <groups:member groups:idRef="MNXM5"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>