Mercurial > repos > tduigou > rptools_rpviz
diff test-data/scored_pathway.xml @ 4:b98c2718a620 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 387d0dd233c1d9948152a2d4af9e69ad10fe1b6a
| author | tduigou |
|---|---|
| date | Thu, 23 Nov 2023 14:27:58 +0000 |
| parents | 9588a5b84518 |
| children |
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--- a/test-data/scored_pathway.xml Thu Nov 02 14:37:19 2023 +0000 +++ b/test-data/scored_pathway.xml Thu Nov 23 14:27:58 2023 +0000 @@ -8,6 +8,9 @@ <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"/> @@ -19,37 +22,29 @@ </compartment> </listOfCompartments> <listOfSpecies> - <species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" 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="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251"> + <rdf:Description rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9"> <bqbiol:is> <rdf:Bag/> </bqbiol:is> </rdf:Description> - <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251"> + <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9"> <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> - <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="_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16" id="CMPD_0000000002" name="CMPD_0000000002" 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="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16"> - <bqbiol:is> - <rdf:Bag/> - </bqbiol:is> - </rdf:Description> - <rdf:BRSynth rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> - <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: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> @@ -68,24 +63,44 @@ <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="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <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="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9"> + <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> <bqbiol:is> <rdf:Bag/> </bqbiol:is> </rdf:Description> - <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9"> + <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> - <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: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> @@ -104,24 +119,72 @@ <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> </annotation> </species> - <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <species metaid="_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16" id="CMPD_0000000002" name="CMPD_0000000002" 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"> + <rdf:Description rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16"> <bqbiol:is> <rdf:Bag/> </bqbiol:is> </rdf:Description> - <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> + <rdf:BRSynth rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16"> <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: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> + </annotation> + </species> + <species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" 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="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="O=C=O"/> + <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/> + <brsynth:inchikey value="CURLTUGMZLYLDI-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> @@ -138,7 +201,10 @@ <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:Bag> + <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.24"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.25"/> + </rdf:Bag> </bqbiol:is> </rdf:Description> <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4"> @@ -197,7 +263,9 @@ <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:Bag> + <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.102"/> + </rdf:Bag> </bqbiol:is> </rdf:Description> <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff"> @@ -317,9 +385,9 @@ </rdf:RDF> </annotation> <groups:listOfMembers> - <groups:member groups:idRef="CMPD_0000000002"/> + <groups:member groups:idRef="TARGET_0000000001"/> <groups:member groups:idRef="MNXM97"/> - <groups:member groups:idRef="TARGET_0000000001"/> + <groups:member groups:idRef="CMPD_0000000002"/> </groups:listOfMembers> </groups:group> <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection"> @@ -332,8 +400,8 @@ </annotation> <groups:listOfMembers> <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM1"/> <groups:member groups:idRef="MNXM15"/> - <groups:member groups:idRef="MNXM1"/> </groups:listOfMembers> </groups:group> <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> @@ -346,9 +414,9 @@ </annotation> <groups:listOfMembers> <groups:member groups:idRef="MNXM13"/> - <groups:member groups:idRef="MNXM15"/> <groups:member groups:idRef="MNXM1"/> <groups:member groups:idRef="MNXM97"/> + <groups:member groups:idRef="MNXM15"/> </groups:listOfMembers> </groups:group> <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" groups:kind="collection">