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annotate physiofit.xml @ 2:232ad69fc93c draft

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planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
author workflow4metabolomics
date Tue, 16 Jan 2024 15:42:03 +0000
parents 52dddad92226
children 4e885e541368
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1 <tool id='physiofit' name='PhysioFit: extracellular flux calculation' version='@TOOL_VERSION@+galaxy0' python_template_version='3.5' profile='21.05'>
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2 <description>PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake and production fluxes</description>
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3 <macros>
2
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4 <token name='@TOOL_VERSION@'>3.3.2</token>
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5 </macros>
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6 <requirements>
2
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7 <requirement type='package' version='@TOOL_VERSION@'>physiofit</requirement>
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8 </requirements>
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9 <command detect_errors='exit_code'><![CDATA[
2
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10 physiofit
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11 --galaxy
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12 --config $configfile
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13 --data $datafile
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14 -or '$recap'
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15 -oz $zip
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16 2> $log
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17 ]]>
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18 </command>
0
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19 <inputs>
2
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20 <param name='datafile' type='data' format='tabular, txt' multiple='true' label='Upload data file containing biomass and concentration values'/>
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21 <param name='configfile' type='data' format='yaml' multiple='true' label='Upload yaml configuration file containing run parameters'/>
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22 </inputs>
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23 <outputs>
2
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24 <data name='recap' label='Summary file' format='csv'/>
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25 <data name='zip' label='Results' format='zip'/>
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26 <data name='log' label='Log' format='txt'/>
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27 </outputs>
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28 <tests>
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29 <test>
2
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30 <param name='datafile' value='data.txt'/>
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31 <param name='configfile' value='config_file.yml'/>
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32 <output name='recap'>
0
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33 <assert_contents>
2
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34 <has_text text='experiments'/>
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35 <has_text text='growth_rate'/>
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36 <has_text text='Glc_q'/>
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37 <has_text text='Glc_M0'/>
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38 <has_text text='Ace_q'/>
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39 <has_text text='Ace_M0'/>
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40 <has_text text='optimal'/>
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41 <has_text text='mean'/>
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42 </assert_contents>
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43 </output>
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44 <output name='zip'>
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45 <assert_contents>
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46 <has_archive_member path='.*\.svg' min='3'/>
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47 <has_archive_member path='.*\.tsv' min='2'/>
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48 <has_archive_member path='.*\.pdf' min='1'/>
0
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49 </assert_contents>
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50 </output>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
2
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54 **PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes**
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55
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56 Fluxes are estimated using mathematical models by fitting time-course measurements of the concentration of
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57 cells and extracellular substrates and products. PhysioFit is shipped with some common growth models, and
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58 additional tailor-made models can be implemented by users.
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59
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60 **PhysioFit includes the following features:**
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61
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62 * **calculation of growth rate and extracellular (uptake and production) fluxes**,
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63 * **a set of steady-state and dynamic models** are shipped with PhysioFit,
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64 * **tailor-made models** can be constructed by users,
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65 * Monte-Carlo sensitivity analysis to **estimate the precision of the calculated fluxes**,
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66 * **evaluation of the goodness of fit and visual inspection of the fitted curves**,
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67 * shipped as a **library** with both a **graphical** and a **command line** interface,
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68 * **open-source, free and easy to install** everywhere where Python 3 and pip run,
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69 * **biologist-friendly**.
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70
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71 It is one of the routine tools that we use at the
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72 `MetaSys team <https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-metasys/>`_
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73 and `MetaToul platform <https://mth-metatoul.com/>`_ to calculate fluxes.
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74
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75 The code is open-source, and available on `GitHub <https://github.com/MetaSys-LISBP/PhysioFit/>`_ under a GPLv3 license.
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76
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77 This documentation is available on Read the Docs (`https://physiofit.readthedocs.io <https://physiofit.readthedocs.io/>`_)
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78 and can be downloaded as a `PDF file <https://readthedocs.org/projects/physiofit/downloads/pdf/latest/>`_.
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79
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80 ]]></help>
0
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81 <citations>
2
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82 <citation type='bibtex'>@article{10.1101/2023.10.12.561695,
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83 author = {Le Grégam, Loïc and Guitton, Yann and Bellvert, Floriant and Heux, Stéphanie and Jourdan, Fabien and Portais, Jean-Charles and Millard, Pierre},
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84 title = "{Physiofit: a software to quantify cell growth parameters and extracellular fluxes}",
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85 year = {2023},
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86 month = {10},
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87 abstract = '{Quantification of growth parameters and extracellular uptake and production fluxes is central in systems and synthetic biology.
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88 Fluxes can be estimated using various mathematical models by fitting time-course measurements of the concentration of cells and
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89 extracellular substrates and products. A single tool is available to calculate extracellular fluxes, but it is hardly interoperable and
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90 includes a single hard-coded growth model. We present our open-source flux calculation software, PhysioFit, which can be used with any
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91 growth model and is interoperable by design. PhysioFit includes by default the most common growth models, and additional models can be
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
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92 implemented by users to calculate fluxes and other growth parameters for metabolic systems or experimental setups that follow alternative
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
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93 kinetics. PhysioFit can be used as a Python library and includes a graphical user interface for intuitive use by end-users and a
232ad69fc93c planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4
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94 command-line interface to streamline integration into existing pipelines.}',
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95 doi = {10.1101/2023.10.12.561695},
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96 url = {https://doi.org/10.1101/2023.10.12.561695},
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97 }
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98 </citation>
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99 </citations>
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100 </tool>