| Previous changeset 0:44e54b56328d (2021-11-24) Next changeset 2:310645d4c5e6 (2022-11-18) |
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Commit message:
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty" |
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modified:
rpthermo.xml test-data/rp_013_0001_with_thermo.xml |
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| diff -r 44e54b56328d -r 21a900eee812 rpthermo.xml --- a/rpthermo.xml Wed Nov 24 09:48:18 2021 +0000 +++ b/rpthermo.xml Wed Feb 09 13:07:30 2022 +0000 |
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| @@ -1,7 +1,10 @@ -<tool id="rpThermo" name="Thermodynamics" version="5.9.2"> +<tool id="rpthermo" name="Thermo" version="@TOOL_VERSION@" profile="19.09"> <description>Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML</description> + <macros> + <token name="@TOOL_VERSION@">5.12.1</token> + </macros> <requirements> - <requirement type="package" version="5.9.2">rptools</requirement> + <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> </requirements> <stdio> <regex match="WARNING:" level="warning" /> @@ -12,18 +15,16 @@ python -m rptools.rpthermo '$input' '$pathway_with_thermo' - --ph '$adv.ph' + --pH '$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" /> + <param name="ph" type="float" value="7.5" min="0" max="14" label="Compartment pH of the pathway" /> + <param name="ionic_strength" type="float" value="0.25" min="0" max="500" label="Compartment ionic strength of the pathway" /> + <param name="pMg" type="float" value="3.0" label="Compartment pMg of the pathway" /> </section> </inputs> <outputs> @@ -34,7 +35,16 @@ <!-- 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"/> + <output name="pathway_with_thermo" file="rp_013_0001_with_thermo.xml" ftype="xml" compare="diff" sort="true" > + <assert_contents> + <is_valid_xml /> + <!--check thermo_dG0_prime value--> + <has_text text="-2308.11630" /> + <!--check thermo_dG value--> + <has_text text="-2151.84763" /> + <has_n_lines n="483" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ @@ -62,7 +72,6 @@ * **--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 --------------------- @@ -72,7 +81,7 @@ Version ---------- -v5.9.2 +v5.12.1 Authors ------- @@ -87,17 +96,6 @@ ]]></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> + <citation type="doi">10.1371/journal.pcbi.1003098</citation> </citations> </tool> \ No newline at end of file |
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| diff -r 44e54b56328d -r 21a900eee812 test-data/rp_013_0001_with_thermo.xml --- a/test-data/rp_013_0001_with_thermo.xml Wed Nov 24 09:48:18 2021 +0000 +++ b/test-data/rp_013_0001_with_thermo.xml Wed Feb 09 13:07:30 2022 +0000 |
| [ |
| b'@@ -23,96 +23,6 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb" id="MNXM6" name="MNXM6" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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)"/>\n- <brsynth:inchikey value="ACFIXJIJDZMPPO-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_5048d67a4507da50d2b6f7a950c531ac5a424ec6d7f1e84da7d56cbbfa7f782e" id="CMPD_0000000004" name="CMPD_0000000004" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_5048d67a4507da50d2b6f7a950c531ac5a424ec6d7f1e84da7d56cbbfa7f782e">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_5048d67a4507da50d2b6f7a950c531ac5a424ec6d7f1e84da7d56cbbfa7f782e">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1[H]"/>\n- <brsynth:inchi value="InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H"/>\n- <brsynth:inchikey value="ISWSIDIOOBJBQZ-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da" id="MNXM4" name="MNXM4" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="O=O"/>\n- <brsynth:inchi value="InChI=1S/O2/c1-2"/>\n- <brsynth:inchikey value="MYMOFIZGZYHOMD-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_000000'..b' <brsynth:thermo_dGm_prime>\n- <brsynth:value value="-947.8047091894496"/>\n+ <brsynth:value value="-948.2158846642606"/>\n <brsynth:error value="10.250976801552927"/>\n <brsynth:units value="kilojoule / mole"/>\n </brsynth:thermo_dGm_prime>\n <brsynth:thermo_dG_prime>\n- <brsynth:value value="-999.1492217936127"/>\n+ <brsynth:value value="-999.5603972684237"/>\n <brsynth:error value="10.250976801552927"/>\n <brsynth:units value="kilojoule / mole"/>\n </brsynth:thermo_dG_prime>\n@@ -376,17 +376,17 @@\n <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n <brsynth:thermo_dG0_prime>\n- <brsynth:value value="-2309.7560063522865"/>\n+ <brsynth:value value="-2308.1163057913755"/>\n <brsynth:error value="22.459032062576664"/>\n <brsynth:units value="kilojoule / mole"/>\n </brsynth:thermo_dG0_prime>\n <brsynth:thermo_dGm_prime>\n- <brsynth:value value="-2309.7560063522865"/>\n+ <brsynth:value value="-2308.1163057913755"/>\n <brsynth:error value="22.459032062576664"/>\n <brsynth:units value="kilojoule / mole"/>\n </brsynth:thermo_dGm_prime>\n <brsynth:thermo_dG_prime>\n- <brsynth:value value="-2309.7560063522865"/>\n+ <brsynth:value value="-2308.1163057913755"/>\n <brsynth:error value="22.459032062576664"/>\n <brsynth:units value="kilojoule / mole"/>\n </brsynth:thermo_dG_prime>\n@@ -428,12 +428,12 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM164"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="MNXM6"/>\n <groups:member groups:idRef="MNXM4"/>\n <groups:member groups:idRef="CMPD_0000000004"/>\n- <groups:member groups:idRef="MNXM6"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n- <groups:member groups:idRef="MNXM164"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -445,10 +445,10 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM1"/>\n+ <groups:member groups:idRef="MNXM5"/>\n <groups:member groups:idRef="MNXM13"/>\n+ <groups:member groups:idRef="MNXM1"/>\n <groups:member groups:idRef="MNXM2"/>\n- <groups:member groups:idRef="MNXM5"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -460,12 +460,12 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM164"/>\n+ <groups:member groups:idRef="MNXM13"/>\n+ <groups:member groups:idRef="MNXM6"/>\n <groups:member groups:idRef="MNXM4"/>\n- <groups:member groups:idRef="MNXM6"/>\n <groups:member groups:idRef="MNXM2"/>\n <groups:member groups:idRef="MNXM1"/>\n- <groups:member groups:idRef="MNXM13"/>\n- <groups:member groups:idRef="MNXM164"/>\n <groups:member groups:idRef="MNXM5"/>\n </groups:listOfMembers>\n </groups:group>\n' |