| Next changeset 1:8057fdd27860 (2022-11-18) |
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Commit message:
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty" |
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added:
rpviz.xml test-data/as_tar_inputs.tgz test-data/lycopene_CrtEBI_from_selenzy.xml test-data/rpviz_single_output.html test-data/rpviz_tar_output.html |
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| diff -r 000000000000 -r ea2ca40a24c5 rpviz.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz.xml Mon Dec 13 17:40:42 2021 +0000 |
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| @@ -0,0 +1,101 @@ +<tool id="rpviz" name="Visualize pathways" version="5.10.0"> + <description>Visualize pathways from the RetroPath Suite</description> + <requirements> + <requirement type="package" version="5.10.0">rptools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #set input_folder="input_folder" + mkdir -p '$input_folder'; + #if str($input_type_conditional.input_type) == "sbml": + #for $input in $input_type_conditional.input_sbml.keys(): + ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml'; + #end for + python -m rptools.rpviz '$input_folder' + #elif str($input_type_conditional.input_type) == "tar": + python -m rptools.rpviz '${input_type_conditional.input_tar}' + #elif str($input_type_conditional.input_type) == "single_sbml": + ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}'; + python -m rptools.rpviz '$input_folder' + #end if + 'out' + #if $adv.cofactor_file + --cofactor '$adv.cofactor_file' + #end if + --autonomous_html '$html_file'; + rm -fr '$input_folder'; + ]]></command> + <inputs> + <conditional name="input_type_conditional"> + <param name="input_type" type="select" label="Source SBML format"> + <option value="tar" selected="True">TAR</option> + <option value="sbml">Collection</option> + <option value="single_sbml">single SBML</option> + </param> + <when value="tar"> + <param name="input_tar" type="data" format="tar" label="Source SBML" /> + </when> + <when value="sbml"> + <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" /> + </when> + <when value="single_sbml"> + <param name="input_single_sbml" type="data" format="xml" label="Source SBML" /> + </when> + </conditional> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="cofactor_file" type="data" format="tsv" optional="true" label="cofactor file" /> + </section> + </inputs> + <outputs> + <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/> + </outputs> + <tests> + <test> + <!-- test 1: check if identical html output is produced (single sbml input) --> + <conditional name="input_type_conditional"> + <param name="input_type" value="single_sbml"/> + <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" /> + </conditional> + <output name="html_file" file="rpviz_single_output.html" compare="sim_size"/> + </test> + <test> + <!-- test 2: check if identical html output is produced (tar input) --> + <conditional name="input_type_conditional"> + <param name="input_type" value="tar"/> + <param name="input_tar" value="as_tar_inputs.tgz" /> + </conditional> + <output name="html_file" file="rpviz_tar_output.html" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +RPVIZ +================ +Visualize pathways from the RetroPath Suite + +Input +----- + +* **input_rpSBMLs**\ : (string) Input file containing rpSBML files in a tar archive or a folder. + +Output +------ + +* **output_folder**\ : (string) Output folder to be used. If it does not exist, an attempt will be made to create it.It the creation of the folder fails, IOError will be raised. +* **autonomous_html**\ : (string) Optional file path, if provided will output an autonomous HTML containing all dependancies. + +Project Links +------------------ + +* `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpviz>`_ + +Version +---------- + +5.10.0 + +License +------- + +* `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ + + ]]></help> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r ea2ca40a24c5 test-data/as_tar_inputs.tgz |
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| Binary file test-data/as_tar_inputs.tgz has changed |
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| diff -r 000000000000 -r ea2ca40a24c5 test-data/lycopene_CrtEBI_from_selenzy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lycopene_CrtEBI_from_selenzy.xml Mon Dec 13 17:40:42 2021 +0000 |
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| b'@@ -0,0 +1,532 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<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">\n+ <model metaid="f9b1ff022aa2133fc1e5e5d1fbac90ac29a744e960a2774be646bc71471ed597" id="RP_model_002_0001" name="002_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">\n+ <listOfCompartments>\n+ <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">\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="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">\n+ <bqbiol:is>\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>\n+ <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed/c"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>\n+ <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </annotation>\n+ </compartment>\n+ </listOfCompartments>\n+ <listOfSpecies>\n+ <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" 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="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles/>\n+ <brsynth:inchi/>\n+ <brsynth:inchikey/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" 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="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H]'..b'es" groups:kind="collection">\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:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="MNXM83"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\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:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM24"/>\n+ <groups:member groups:idRef="MNXM11"/>\n+ <groups:member groups:idRef="MNXM8975"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\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:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM11"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" groups:kind="collection">\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:BRSynth rdf:about="#a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM24"/>\n+ <groups:member groups:idRef="MNXM8975"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection">\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:BRSynth rdf:about="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="MNXM24"/>\n+ <groups:member groups:idRef="MNXM8975"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ </groups:listOfGroups>\n+ </model>\n+</sbml>\n' |
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| diff -r 000000000000 -r ea2ca40a24c5 test-data/rpviz_single_output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rpviz_single_output.html Mon Dec 13 17:40:42 2021 +0000 |
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| b'@@ -0,0 +1,6560 @@\n+<!DOCTYPE html>\n+\n+<!--\n+__author__ = \'Thomas Duigou (thomas.duigou@inra.fr)\'\n+__license__ = \'MIT\'\n+-->\n+\n+<html lang="en">\n+<head>\n+ <meta charset="utf-8">\n+ <meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1"/>\n+\n+ <title>Pathway viewer</title>\n+\n+ <!-- Local libraries -->\n+ <script >/*! jQuery v3.6.0 | (c) OpenJS Foundation and other contributors | jquery.org/license */\n+!function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined"!=typeof window?window:this,function(C,e){"use strict";var t=[],r=Object.getPrototypeOf,s=t.slice,g=t.flat?function(e){return t.flat.call(e)}:function(e){return 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n=+t.length,r=0,i=e.length;r<n;r++)e[i++]=t[r];return e.length=i,e},grep:function(e,t,n){for(var r=[],i=0,o=e.length,a=!n;i<o;i++)!t(e[i],i)!==a&&r.push(e[i]);return r},map:function(e,t,n){var r,i,o=0,a=[];if(p(e))for(r=e.length;o<r;o++)null!=(i=t'..b'+ <div class="raw-text reaction_info_pathids"></div>\n+ </div>\n+ <!-- UniProt IDs -->\n+ <div>\n+ <div class="info-subtitle">UniProt IDs (Selenzyme score)</div>\n+ <div class="raw-text reaction_info_uniprot_crosslinks"></div>\n+ </div>\n+ <!-- Crosslink to Selenzyme -->\n+ <div>\n+ <div class="info-subtitle">Enzyme selection</div>\n+ <div class="raw-text"><span class="reaction_info_selenzyme_crosslink"></span></div>\n+ </div>\n+ </div>\n+ <!-- Information on a selected pathway -->\n+ <div id="panel_pathway_info">\n+ <div class="info-title">Pathway</div>\n+ <div class="info-name"><span class="pathway_info_path_id"></span></div>\n+ <div class="spacer"></div>\n+ <!-- Pathway ID -->\n+ <div>\n+ <div class="info-subtitle">Pathway ID</div>\n+ <div class="raw-text"><span class="pathway_info_path_id"></span></div>\n+ </div>\n+ <!-- Number of steps -->\n+ <div>\n+ <div class="info-subtitle">Number of steps</div>\n+ <div class="raw-text"><span class="pathway_info_nb_steps"></span></div>\n+ </div>\n+ <!-- Thermodynamic -->\n+ <div>\n+ <div class="info-subtitle">Δ<sub>r</sub>G\' (kJ/mol)</div>\n+ <div class="raw-text"><span class="pathway_info_thermo"></span></div>\n+ </div>\n+ <!-- Rule score -->\n+ <div>\n+ <div class="info-subtitle">Rule score</div>\n+ <div class="raw-text"><span class="pathway_info_rule_score"></span></div>\n+ </div>\n+ <!-- FBA -->\n+ <div>\n+ <div class="info-subtitle">Target\'s production flux (mmol gDW<sup>-1</sup> hr<sup>-1</sup>)</div>\n+ <div class="raw-text"><span class="pathway_info_target_flux"></span></div>\n+ </div>\n+ <!-- Global score -->\n+ <div>\n+ <div class="info-subtitle">Global score</div>\n+ <div class="raw-text"><span class="pathway_info_global_score"></span></div>\n+ </div>\n+ </div>\n+ <!-- In dev stuff -->\n+ <!-- <div>Information</div>\n+ <div id="react_img" class="pointer"></div>\n+ <div id="reversibility" class=\'inf2\'></div>\n+ <input id="thermo_button" type="button" value="Thermodynamics"/>\n+ <input id="flux_button" type="button" value="Flux"/>\n+ <div id="rule" style="display:none;" class="boxinf">\n+ <div id="sub_rule_score" class="inf2">Rule Score</div>\n+ </div>\n+ <div id="thermo"style="display:none;" class="boxinf"></div>\n+ <div id="flux"style="display:none;" class="boxinf">\n+ <div id="sub_fba" class="inf2">FBA (mmol/gDW/h)</div>\n+ <div id="sub_fba_obj" class="inf1">FBA biomass objective</div>\n+ </div>\n+ <div id="selenzyme-link"></div>\n+ <div id="selenzyme_table"></div> -->\n+ </div>\n+\n+ </div>\n+ </div>\n+\n+ </div>\n+\n+</body>\n+</html>\n' |
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| diff -r 000000000000 -r ea2ca40a24c5 test-data/rpviz_tar_output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rpviz_tar_output.html Mon Dec 13 17:40:42 2021 +0000 |
| [ |
| b'@@ -0,0 +1,7436 @@\n+<!DOCTYPE html>\n+\n+<!--\n+__author__ = \'Thomas Duigou (thomas.duigou@inra.fr)\'\n+__license__ = \'MIT\'\n+-->\n+\n+<html lang="en">\n+<head>\n+ <meta charset="utf-8">\n+ <meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1"/>\n+\n+ <title>Pathway viewer</title>\n+\n+ <!-- Local libraries -->\n+ <script >/*! jQuery v3.6.0 | (c) OpenJS Foundation and other contributors | jquery.org/license */\n+!function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined"!=typeof window?window:this,function(C,e){"use strict";var t=[],r=Object.getPrototypeOf,s=t.slice,g=t.flat?function(e){return t.flat.call(e)}:function(e){return 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n=+t.length,r=0,i=e.length;r<n;r++)e[i++]=t[r];return e.length=i,e},grep:function(e,t,n){for(var r=[],i=0,o=e.length,a=!n;i<o;i++)!t(e[i],i)!==a&&r.push(e[i]);return r},map:function(e,t,n){var r,i,o=0,a=[];if(p(e))for(r=e.length;o<r;o++)null!=(i=t'..b'+ <div class="raw-text reaction_info_pathids"></div>\n+ </div>\n+ <!-- UniProt IDs -->\n+ <div>\n+ <div class="info-subtitle">UniProt IDs (Selenzyme score)</div>\n+ <div class="raw-text reaction_info_uniprot_crosslinks"></div>\n+ </div>\n+ <!-- Crosslink to Selenzyme -->\n+ <div>\n+ <div class="info-subtitle">Enzyme selection</div>\n+ <div class="raw-text"><span class="reaction_info_selenzyme_crosslink"></span></div>\n+ </div>\n+ </div>\n+ <!-- Information on a selected pathway -->\n+ <div id="panel_pathway_info">\n+ <div class="info-title">Pathway</div>\n+ <div class="info-name"><span class="pathway_info_path_id"></span></div>\n+ <div class="spacer"></div>\n+ <!-- Pathway ID -->\n+ <div>\n+ <div class="info-subtitle">Pathway ID</div>\n+ <div class="raw-text"><span class="pathway_info_path_id"></span></div>\n+ </div>\n+ <!-- Number of steps -->\n+ <div>\n+ <div class="info-subtitle">Number of steps</div>\n+ <div class="raw-text"><span class="pathway_info_nb_steps"></span></div>\n+ </div>\n+ <!-- Thermodynamic -->\n+ <div>\n+ <div class="info-subtitle">Δ<sub>r</sub>G\' (kJ/mol)</div>\n+ <div class="raw-text"><span class="pathway_info_thermo"></span></div>\n+ </div>\n+ <!-- Rule score -->\n+ <div>\n+ <div class="info-subtitle">Rule score</div>\n+ <div class="raw-text"><span class="pathway_info_rule_score"></span></div>\n+ </div>\n+ <!-- FBA -->\n+ <div>\n+ <div class="info-subtitle">Target\'s production flux (mmol gDW<sup>-1</sup> hr<sup>-1</sup>)</div>\n+ <div class="raw-text"><span class="pathway_info_target_flux"></span></div>\n+ </div>\n+ <!-- Global score -->\n+ <div>\n+ <div class="info-subtitle">Global score</div>\n+ <div class="raw-text"><span class="pathway_info_global_score"></span></div>\n+ </div>\n+ </div>\n+ <!-- In dev stuff -->\n+ <!-- <div>Information</div>\n+ <div id="react_img" class="pointer"></div>\n+ <div id="reversibility" class=\'inf2\'></div>\n+ <input id="thermo_button" type="button" value="Thermodynamics"/>\n+ <input id="flux_button" type="button" value="Flux"/>\n+ <div id="rule" style="display:none;" class="boxinf">\n+ <div id="sub_rule_score" class="inf2">Rule Score</div>\n+ </div>\n+ <div id="thermo"style="display:none;" class="boxinf"></div>\n+ <div id="flux"style="display:none;" class="boxinf">\n+ <div id="sub_fba" class="inf2">FBA (mmol/gDW/h)</div>\n+ <div id="sub_fba_obj" class="inf1">FBA biomass objective</div>\n+ </div>\n+ <div id="selenzyme-link"></div>\n+ <div id="selenzyme_table"></div> -->\n+ </div>\n+\n+ </div>\n+ </div>\n+\n+ </div>\n+\n+</body>\n+</html>\n' |