Mercurial > repos > tduigou > rptools_rpcompletion

comparison test-data/scored_pathway.xml @ 1:c33bde07cbc7 draft default tip

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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
comparison
equal deleted inserted replaced
0:874093da8436 1:c33bde07cbc7
12 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/> 12 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
13 <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/> 13 <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
14 <rdf:li rdf:resource="http://identifiers.org/seed/c"/> 14 <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
15 <rdf:li rdf:resource="http://identifiers.org/seed/c0"/> 15 <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
16 <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/> 16 <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
17 <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
18 </rdf:Bag> 17 </rdf:Bag>
19 </bqbiol:is> 18 </bqbiol:is>
20 </rdf:Description> 19 </rdf:Description>
21 </rdf:RDF> 20 </rdf:RDF>
22 </annotation> 21 </annotation>
34 <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9"> 33 <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
35 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> 34 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
36 <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/> 35 <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
37 <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)"/> 36 <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)"/>
38 <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/> 37 <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/>
38 <brsynth:fba_biomass_shadow_price>
39 <brsynth:value value="None"/>
40 </brsynth:fba_biomass_shadow_price>
41 <brsynth:fba_fraction_shadow_price>
42 <brsynth:value value="None"/>
43 </brsynth:fba_fraction_shadow_price>
44 <brsynth:thermo_standard_dg_formation>
45 <brsynth:value value="-207.07052002003908"/>
46 <brsynth:units value="kilojoule / mole"/>
47 </brsynth:thermo_standard_dg_formation>
48 </brsynth:brsynth>
49 </rdf:BRSynth>
50 </rdf:RDF>
51 </annotation>
52 </species>
53 <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
54 <annotation>
55 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
56 <rdf:Description rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
57 <bqbiol:is>
58 <rdf:Bag/>
59 </bqbiol:is>
60 </rdf:Description>
61 <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
62 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
63 <brsynth:smiles value="N"/>
64 <brsynth:inchi value="InChI=1S/H3N/h1H3"/>
65 <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
66 <brsynth:fba_biomass_shadow_price>
67 <brsynth:value value="None"/>
68 </brsynth:fba_biomass_shadow_price>
69 <brsynth:fba_fraction_shadow_price>
70 <brsynth:value value="None"/>
71 </brsynth:fba_fraction_shadow_price>
72 <brsynth:thermo_standard_dg_formation>
73 <brsynth:value value="-81.91776181003092"/>
74 <brsynth:units value="kilojoule / mole"/>
75 </brsynth:thermo_standard_dg_formation>
76 </brsynth:brsynth>
77 </rdf:BRSynth>
78 </rdf:RDF>
79 </annotation>
80 </species>
81 <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
82 <annotation>
83 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
84 <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
85 <bqbiol:is>
86 <rdf:Bag/>
87 </bqbiol:is>
88 </rdf:Description>
89 <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
90 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
91 <brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
92 <brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/>
93 <brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/>
94 <brsynth:fba_biomass_shadow_price>
95 <brsynth:value value="-0.0"/>
96 </brsynth:fba_biomass_shadow_price>
97 <brsynth:fba_fraction_shadow_price>
98 <brsynth:value value="-1.0"/>
99 </brsynth:fba_fraction_shadow_price>
100 <brsynth:thermo_standard_dg_formation>
101 <brsynth:value value="208.92559504464236"/>
102 <brsynth:units value="kilojoule / mole"/>
103 </brsynth:thermo_standard_dg_formation>
104 </brsynth:brsynth>
105 </rdf:BRSynth>
106 </rdf:RDF>
107 </annotation>
108 </species>
109 <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
110 <annotation>
111 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
112 <rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
113 <bqbiol:is>
114 <rdf:Bag/>
115 </bqbiol:is>
116 </rdf:Description>
117 <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
118 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
119 <brsynth:smiles value="[H+]"/>
120 <brsynth:inchi value="InChI=1S/p+1"/>
121 <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
122 <brsynth:fba_biomass_shadow_price>
123 <brsynth:value value="None"/>
124 </brsynth:fba_biomass_shadow_price>
125 <brsynth:fba_fraction_shadow_price>
126 <brsynth:value value="None"/>
127 </brsynth:fba_fraction_shadow_price>
128 <brsynth:thermo_standard_dg_formation>
129 <brsynth:value value="NaN"/>
130 <brsynth:units value="kilojoule / mole"/>
131 </brsynth:thermo_standard_dg_formation>
39 </brsynth:brsynth> 132 </brsynth:brsynth>
40 </rdf:BRSynth> 133 </rdf:BRSynth>
41 </rdf:RDF> 134 </rdf:RDF>
42 </annotation> 135 </annotation>
43 </species> 136 </species>
52 <rdf:BRSynth rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16"> 145 <rdf:BRSynth rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16">
53 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> 146 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
54 <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> 147 <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
55 <brsynth:inchi value="InChI=1S/C9H8O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-7H,(H,10,11)"/> 148 <brsynth:inchi value="InChI=1S/C9H8O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-7H,(H,10,11)"/>
56 <brsynth:inchikey value="WBYWAXJHAXSJNI-UHFFFAOYSA-N"/> 149 <brsynth:inchikey value="WBYWAXJHAXSJNI-UHFFFAOYSA-N"/>
150 <brsynth:fba_biomass_shadow_price>
151 <brsynth:value value="-0.0009404190769783985"/>
152 </brsynth:fba_biomass_shadow_price>
153 <brsynth:fba_fraction_shadow_price>
154 <brsynth:value value="-1.0057339449541285"/>
155 </brsynth:fba_fraction_shadow_price>
156 <brsynth:thermo_standard_dg_formation>
157 <brsynth:value value="-127.1962856224608"/>
158 <brsynth:units value="kilojoule / mole"/>
159 </brsynth:thermo_standard_dg_formation>
57 </brsynth:brsynth> 160 </brsynth:brsynth>
58 </rdf:BRSynth> 161 </rdf:BRSynth>
59 </rdf:RDF> 162 </rdf:RDF>
60 </annotation> 163 </annotation>
61 </species> 164 </species>
70 <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251"> 173 <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
71 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> 174 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
72 <brsynth:smiles value="O=C=O"/> 175 <brsynth:smiles value="O=C=O"/>
73 <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/> 176 <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/>
74 <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/> 177 <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/>
75 </brsynth:brsynth> 178 <brsynth:fba_biomass_shadow_price>
76 </rdf:BRSynth> 179 <brsynth:value value="None"/>
77 </rdf:RDF> 180 </brsynth:fba_biomass_shadow_price>
78 </annotation> 181 <brsynth:fba_fraction_shadow_price>
79 </species> 182 <brsynth:value value="None"/>
80 <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> 183 </brsynth:fba_fraction_shadow_price>
81 <annotation> 184 <brsynth:thermo_standard_dg_formation>
82 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> 185 <brsynth:value value="-386.0000000000019"/>
83 <rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25"> 186 <brsynth:units value="kilojoule / mole"/>
84 <bqbiol:is> 187 </brsynth:thermo_standard_dg_formation>
85 <rdf:Bag/>
86 </bqbiol:is>
87 </rdf:Description>
88 <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
89 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
90 <brsynth:smiles value="[H+]"/>
91 <brsynth:inchi value="InChI=1S/p+1"/>
92 <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
93 </brsynth:brsynth>
94 </rdf:BRSynth>
95 </rdf:RDF>
96 </annotation>
97 </species>
98 <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
99 <annotation>
100 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
101 <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
102 <bqbiol:is>
103 <rdf:Bag/>
104 </bqbiol:is>
105 </rdf:Description>
106 <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
107 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
108 <brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
109 <brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/>
110 <brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/>
111 </brsynth:brsynth>
112 </rdf:BRSynth>
113 </rdf:RDF>
114 </annotation>
115 </species>
116 <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
117 <annotation>
118 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
119 <rdf:Description rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
120 <bqbiol:is>
121 <rdf:Bag/>
122 </bqbiol:is>
123 </rdf:Description>
124 <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
125 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
126 <brsynth:smiles value="N"/>
127 <brsynth:inchi value="InChI=1S/H3N/h1H3"/>
128 <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
129 </brsynth:brsynth> 188 </brsynth:brsynth>
130 </rdf:BRSynth> 189 </rdf:BRSynth>
131 </rdf:RDF> 190 </rdf:RDF>
132 </annotation> 191 </annotation>
133 </species> 192 </species>
354 </rdf:RDF> 413 </rdf:RDF>
355 </annotation> 414 </annotation>
356 <groups:listOfMembers> 415 <groups:listOfMembers>
357 <groups:member groups:idRef="MNXM13"/> 416 <groups:member groups:idRef="MNXM13"/>
358 <groups:member groups:idRef="MNXM1"/> 417 <groups:member groups:idRef="MNXM1"/>
418 <groups:member groups:idRef="MNXM97"/>
359 <groups:member groups:idRef="MNXM15"/> 419 <groups:member groups:idRef="MNXM15"/>
360 <groups:member groups:idRef="MNXM97"/>
361 </groups:listOfMembers> 420 </groups:listOfMembers>
362 </groups:group> 421 </groups:group>
363 <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" groups:kind="collection"> 422 <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" groups:kind="collection">
364 <annotation> 423 <annotation>
365 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> 424 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">