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@@ -0,0 +1,103 @@
+<tool id="rpThermo" name="Thermodynamics" version="5.9.2">
+    <description>Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML</description>
+    <requirements>
+        <requirement type="package" version="5.9.2">rptools</requirement>
+    </requirements>
+    <stdio>
+        <regex match="WARNING:" level="warning" />
+        <regex match="ERROR:" level="fatal" />
+        <regex match="ERROR:root:ChemAxon" level="warning" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rptools.rpthermo
+        '$input'
+        '$pathway_with_thermo' 
+        --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" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="pathway_with_thermo" format="xml" label="${tool.name} - ${input.name}" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- 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"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Thermodynamics
+===============
+Calculate the formation energy of chemical species either using an internal database or estimate it by decomposing them using the `component contribution <https://gitlab.com/elad.noor/component-contribution>`_ method. Thereafter this tool predicts the Gibbs free energy of reactions and of the whole heterologous pathway by combining the formation energy of each individual compound.
+
+.. image:: https://raw.githubusercontent.com/Galaxy-SynBioCAD/rpThermo/standalone/galaxy/img/rpThermo.png 
+	:width: 80 %
+	:align: center
+
+
+|
+
+
+Above is an illustration of the Gibbs free energy calculation using the component contribution package. The color-coded arrows from red (best) to blue (worst) show the best and worst-performing reactions.
+
+Required:
+
+* **input**\ : (string) Path to the input file
+* **output**\ : (string) Path to the output file 
+
+Advanced Options:
+
+* **--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
+---------------------
+
+* `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpthermo>`_
+
+Version
+----------
+
+v5.9.2
+
+Authors
+-------
+
+* **Melchior du Lac** 
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+* Joan Hérisson
+
+    ]]></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>
+    </citations>
+</tool>
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