# HG changeset patch
# User tduigou
# Date 1644412050 0
# Node ID 21a900eee812dd8590e88f48bcc845390cb7fb08
# Parent  44e54b56328d48391c36364713dd60d3e58dac8f
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

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
@@ -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
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
@@ -23,96 +23,6 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species metaid="_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb" id="MNXM6" name="MNXM6" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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-              <bqbiol:is>
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-              </bqbiol:is>
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-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
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-                <brsynth:inchi value="InChI=1S/p+1"/>
-                <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
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       <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/">
@@ -149,19 +59,55 @@
           </rdf:RDF>
         </annotation>
       </species>
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+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
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-            <rdf:Description rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
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               <bqbiol:is>
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-            <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
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+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1O[H]"/>
+                <brsynth:inchi value="InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H"/>
+                <brsynth:inchikey value="YCIMNLLNPGFGHC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
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+      <species metaid="_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb" id="MNXM6" name="MNXM6" 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="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
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+            <rdf:BRSynth rdf:about="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb">
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-                <brsynth:inchikey value="FJKROLUGYXJWQN-UHFFFAOYSA-N"/>
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+                <brsynth:inchikey value="ACFIXJIJDZMPPO-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
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+        </annotation>
+      </species>
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+        <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="#c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
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+                <brsynth:inchi value="InChI=1S/O2/c1-2"/>
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@@ -185,6 +131,60 @@
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         </annotation>
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+                <brsynth:smiles value="[H+]"/>
+                <brsynth:inchi value="InChI=1S/p+1"/>
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+                <brsynth:inchikey value="ISWSIDIOOBJBQZ-UHFFFAOYSA-N"/>
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+        <annotation>
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+              <bqbiol:is>
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+                <brsynth:inchikey value="FJKROLUGYXJWQN-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="_4a3e4e32a6db24e5ddaa18997f93519c4ef1c0172e96160cd56ad49ecf025995" id="MNXM5" name="MNXM5" 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/">
@@ -228,17 +228,17 @@
                 <brsynth:rule_score value="0.7023718970192103"/>
                 <brsynth:idx_in_path value="1"/>
                 <brsynth:thermo_dG0_prime>
-                  <brsynth:value value="-289.68604442151195"/>
+                  <brsynth:value value="-288.7061190195177"/>
                   <brsynth:error value="7.140374782195817"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dG0_prime>
                 <brsynth:thermo_dGm_prime>
-                  <brsynth:value value="-323.915719490954"/>
+                  <brsynth:value value="-322.93579408895977"/>
                   <brsynth:error value="7.140374782195817"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dGm_prime>
                 <brsynth:thermo_dG_prime>
-                  <brsynth:value value="-289.68604442151195"/>
+                  <brsynth:value value="-288.7061190195177"/>
                   <brsynth:error value="7.140374782195817"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dG_prime>
@@ -284,17 +284,17 @@
                 <brsynth:rule_score value="0.5683242688496836"/>
                 <brsynth:idx_in_path value="2"/>
                 <brsynth:thermo_dG0_prime>
-                  <brsynth:value value="-294.3657675294261"/>
+                  <brsynth:value value="-294.9583676429335"/>
                   <brsynth:error value="9.81314488510582"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dG0_prime>
                 <brsynth:thermo_dGm_prime>
-                  <brsynth:value value="-260.136092459984"/>
+                  <brsynth:value value="-260.72869257349146"/>
                   <brsynth:error value="9.81314488510582"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dGm_prime>
                 <brsynth:thermo_dG_prime>
-                  <brsynth:value value="-294.3657675294261"/>
+                  <brsynth:value value="-294.9583676429335"/>
                   <brsynth:error value="9.81314488510582"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dG_prime>
@@ -335,17 +335,17 @@
                 <brsynth:rule_score value="0.5982208769718989"/>
                 <brsynth:idx_in_path value="3"/>
                 <brsynth:thermo_dG0_prime>
-                  <brsynth:value value="-999.1492217936127"/>
+                  <brsynth:value value="-999.5603972684237"/>
                   <brsynth:error value="10.250976801552927"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dG0_prime>
                 <brsynth:thermo_dGm_prime>
-                  <brsynth:value value="-947.8047091894496"/>
+                  <brsynth:value value="-948.2158846642606"/>
                   <brsynth:error value="10.250976801552927"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dGm_prime>
                 <brsynth:thermo_dG_prime>
-                  <brsynth:value value="-999.1492217936127"/>
+                  <brsynth:value value="-999.5603972684237"/>
                   <brsynth:error value="10.250976801552927"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dG_prime>
@@ -376,17 +376,17 @@
             <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                 <brsynth:thermo_dG0_prime>
-                  <brsynth:value value="-2309.7560063522865"/>
+                  <brsynth:value value="-2308.1163057913755"/>
                   <brsynth:error value="22.459032062576664"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dG0_prime>
                 <brsynth:thermo_dGm_prime>
-                  <brsynth:value value="-2309.7560063522865"/>
+                  <brsynth:value value="-2308.1163057913755"/>
                   <brsynth:error value="22.459032062576664"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dGm_prime>
                 <brsynth:thermo_dG_prime>
-                  <brsynth:value value="-2309.7560063522865"/>
+                  <brsynth:value value="-2308.1163057913755"/>
                   <brsynth:error value="22.459032062576664"/>
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dG_prime>
@@ -428,12 +428,12 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM164"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+          <groups:member groups:idRef="MNXM6"/>
           <groups:member groups:idRef="MNXM4"/>
           <groups:member groups:idRef="CMPD_0000000004"/>
-          <groups:member groups:idRef="MNXM6"/>
-          <groups:member groups:idRef="CMPD_0000000003"/>
-          <groups:member groups:idRef="MNXM164"/>
-          <groups:member groups:idRef="TARGET_0000000001"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -445,10 +445,10 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
-          <groups:member groups:idRef="MNXM1"/>
+          <groups:member groups:idRef="MNXM5"/>
           <groups:member groups:idRef="MNXM13"/>
+          <groups:member groups:idRef="MNXM1"/>
           <groups:member groups:idRef="MNXM2"/>
-          <groups:member groups:idRef="MNXM5"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -460,12 +460,12 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM164"/>
+          <groups:member groups:idRef="MNXM13"/>
+          <groups:member groups:idRef="MNXM6"/>
           <groups:member groups:idRef="MNXM4"/>
-          <groups:member groups:idRef="MNXM6"/>
           <groups:member groups:idRef="MNXM2"/>
           <groups:member groups:idRef="MNXM1"/>
-          <groups:member groups:idRef="MNXM13"/>
-          <groups:member groups:idRef="MNXM164"/>
           <groups:member groups:idRef="MNXM5"/>
         </groups:listOfMembers>
       </groups:group>