Mercurial > repos > tduigou > rptools_rpcompletion
diff test-data/scored_pathway.xml @ 1:c33bde07cbc7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit c1b249f25f3143e21980cd7daecb1aebb88ef948-dirty
| author | tduigou |
|---|---|
| date | Fri, 24 Oct 2025 08:37:01 +0000 |
| parents | 874093da8436 |
| children |
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--- a/test-data/scored_pathway.xml Tue Mar 28 12:05:15 2023 +0000 +++ b/test-data/scored_pathway.xml Fri Oct 24 08:37:01 2025 +0000 @@ -14,7 +14,6 @@ <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> @@ -36,6 +35,100 @@ <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/> <brsynth:inchi value="InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"/> <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/> + <brsynth:fba_biomass_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_biomass_shadow_price> + <brsynth:fba_fraction_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_fraction_shadow_price> + <brsynth:thermo_standard_dg_formation> + <brsynth:value value="-207.07052002003908"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" 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="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="N"/> + <brsynth:inchi value="InChI=1S/H3N/h1H3"/> + <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/> + <brsynth:fba_biomass_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_biomass_shadow_price> + <brsynth:fba_fraction_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_fraction_shadow_price> + <brsynth:thermo_standard_dg_formation> + <brsynth:value value="-81.91776181003092"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" 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="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> + <brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/> + <brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/> + <brsynth:fba_biomass_shadow_price> + <brsynth:value value="-0.0"/> + </brsynth:fba_biomass_shadow_price> + <brsynth:fba_fraction_shadow_price> + <brsynth:value value="-1.0"/> + </brsynth:fba_fraction_shadow_price> + <brsynth:thermo_standard_dg_formation> + <brsynth:value value="208.92559504464236"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" 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="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H+]"/> + <brsynth:inchi value="InChI=1S/p+1"/> + <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/> + <brsynth:fba_biomass_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_biomass_shadow_price> + <brsynth:fba_fraction_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_fraction_shadow_price> + <brsynth:thermo_standard_dg_formation> + <brsynth:value value="NaN"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> </brsynth:brsynth> </rdf:BRSynth> </rdf:RDF> @@ -54,6 +147,16 @@ <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> <brsynth:inchi value="InChI=1S/C9H8O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-7H,(H,10,11)"/> <brsynth:inchikey value="WBYWAXJHAXSJNI-UHFFFAOYSA-N"/> + <brsynth:fba_biomass_shadow_price> + <brsynth:value value="-0.0009404190769783985"/> + </brsynth:fba_biomass_shadow_price> + <brsynth:fba_fraction_shadow_price> + <brsynth:value value="-1.0057339449541285"/> + </brsynth:fba_fraction_shadow_price> + <brsynth:thermo_standard_dg_formation> + <brsynth:value value="-127.1962856224608"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> </brsynth:brsynth> </rdf:BRSynth> </rdf:RDF> @@ -72,60 +175,16 @@ <brsynth:smiles value="O=C=O"/> <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/> <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/> - </brsynth:brsynth> - </rdf:BRSynth> - </rdf:RDF> - </annotation> - </species> - <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" 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="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25"> - <bqbiol:is> - <rdf:Bag/> - </bqbiol:is> - </rdf:Description> - <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> - <brsynth:smiles value="[H+]"/> - <brsynth:inchi value="InChI=1S/p+1"/> - <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/> - </brsynth:brsynth> - </rdf:BRSynth> - </rdf:RDF> - </annotation> - </species> - <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" 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="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> - <bqbiol:is> - <rdf:Bag/> - </bqbiol:is> - </rdf:Description> - <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> - <brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> - <brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/> - <brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/> - </brsynth:brsynth> - </rdf:BRSynth> - </rdf:RDF> - </annotation> - </species> - <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" 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="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b"> - <bqbiol:is> - <rdf:Bag/> - </bqbiol:is> - </rdf:Description> - <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> - <brsynth:smiles value="N"/> - <brsynth:inchi value="InChI=1S/H3N/h1H3"/> - <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/> + <brsynth:fba_biomass_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_biomass_shadow_price> + <brsynth:fba_fraction_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_fraction_shadow_price> + <brsynth:thermo_standard_dg_formation> + <brsynth:value value="-386.0000000000019"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> </brsynth:brsynth> </rdf:BRSynth> </rdf:RDF> @@ -356,8 +415,8 @@ <groups:listOfMembers> <groups:member groups:idRef="MNXM13"/> <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM97"/> <groups:member groups:idRef="MNXM15"/> - <groups:member groups:idRef="MNXM97"/> </groups:listOfMembers> </groups:group> <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" groups:kind="collection">