# HG changeset patch
# User tduigou
# Date 1637747298 0
# Node ID 44e54b56328d48391c36364713dd60d3e58dac8f
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
diff -r 000000000000 -r 44e54b56328d rpthermo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpthermo.xml Wed Nov 24 09:48:18 2021 +0000
@@ -0,0 +1,103 @@
+
+ Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML
+
+ rptools
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+ `_ 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
+
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+|
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+
+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 `_
+
+Version
+----------
+
+v5.9.2
+
+Authors
+-------
+
+* **Melchior du Lac**
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+* Joan Hérisson
+
+ ]]>
+
+
+@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}
+}
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 44e54b56328d test-data/rp_013_0001.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rp_013_0001.xml Wed Nov 24 09:48:18 2021 +0000
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diff -r 000000000000 -r 44e54b56328d test-data/rp_013_0001_with_thermo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rp_013_0001_with_thermo.xml Wed Nov 24 09:48:18 2021 +0000
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