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author tduigou
date Fri, 18 Nov 2022 16:21:05 +0000
parents ec49df43ffae
children
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1 <tool id="rpthermo" name="Thermo" version="@TOOL_VERSION@" profile="21.09">
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2 <description>Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">6.0.1</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
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8 </requirements>
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9 <stdio>
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10 <regex match="WARNING:" level="warning" />
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11 <regex match="ERROR:" level="fatal" />
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12 <regex match="ERROR:root:ChemAxon" level="warning" />
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 python -m rptools.rpthermo
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16 '$input'
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17 '$pathway_with_thermo'
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18 --pH '$adv.ph'
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19 --ionic_strength '$adv.ionic_strength'
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20 --pMg '$adv.pMg'
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21 ]]></command>
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22 <inputs>
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23 <param name="input" type="data" format="sbml" label="SBML Input File" help="Pathways in SBML format" />
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24 <section name="adv" title="Advanced Options" expanded="false">
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25 <param name="ph" type="float" value="7.5" min="0" max="14" label="Compartment pH of the pathway" />
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26 <param name="ionic_strength" type="float" value="0.25" min="0" max="500" label="Compartment ionic strength of the pathway" />
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27 <param name="pMg" type="float" value="3.0" label="Compartment pMg (Magnesium vapor pressure) of the pathway" />
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28 </section>
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29 </inputs>
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30 <outputs>
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31 <data name="pathway_with_thermo" format="xml" label="${tool.name} - ${input.name}" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <!-- test 1: check if identical outputs are produced with default parameters -->
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36 <param name="input" value="rp_013_0001.xml" />
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37 <param name="model" value="e_coli_iML1515.sbml" />
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38 <output name="pathway_with_thermo" file="rp_013_0001_with_thermo.xml" ftype="xml" compare="diff" sort="true" >
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39 <assert_contents>
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40 <is_valid_xml />
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41 <!--check thermo_dG0_prime value-->
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42 <has_text text="-2308.11630" />
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43 <!--check thermo_dG value-->
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44 <has_text text="-2151.84763" />
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45 <has_n_lines n="483" />
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46 </assert_contents>
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47 </output>
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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51 Thermodynamics
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52 ===============
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53 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.
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54
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55 The goal of the thermodynamic analysis is to estimate the feasibility of the predicted pathways toward target production, in physiological conditions (PH, ionic strength).
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56
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57 .. image:: https://raw.githubusercontent.com/Galaxy-SynBioCAD/rpThermo/standalone/galaxy/img/rpThermo.png
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58 :width: 80 %
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59 :align: center
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60
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62 |
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63
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64
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65 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.
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66
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67 Required:
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68
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69 Inputs
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70 ------
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71
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72 * **SBML Input File**\ : Pathways in SBML format
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73
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74 Advanced Options:
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75
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76 * **PH**\ :(float) Compartment PH of the pathway
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77 * **Ionic strength**\ :(float) Compartment ionic strength of the pathway
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78 * **pMg**\ :(float) Compartment pMg (Magnesium vapor pressure) of the pathway
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79
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80 Output
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81 ------
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82
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83 * **Pathway with thermo**\ : annotated pathways (with thermodynamics information for each reaction) in SBML(Systems Biology Markup Language) format.
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84
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85 Project Links
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86 ---------------------
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87
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88 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpthermo>`_
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89
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90 Acknowledgments
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91 ---------------
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92
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93 * Thomas Duigou
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94 * Joan Hérisson
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95
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96 ]]></help>
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97 <citations>
1
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98 <citation type="doi">10.1371/journal.pcbi.1003098</citation>
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99 </citations>
2
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100 <creator>
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101 <person givenName="Melchior" familyName="du Lac" identifier="https://orcid.org/0000-0002-9984-4689" />
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102 </creator>
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103 </tool>