comparison physiofit.xml @ 2:232ad69fc93c draft

planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4

1:52dddad92226

<tool id='physiofit' name='PhysioFit' profile='21.09' version='@TOOL_VERSION@+galaxy0' python_template_version='3.5'>
    <description>Extracellular flux analysis</description>
    <macros>
        <token name="@TOOL_VERSION@">2.2.1</token>
    </macros>
    <requirements>
        <requirement type='package' version='@TOOL_VERSION@'>physiofit4galaxy</requirement>
    </requirements>
    <command detect_errors='exit_code'><![CDATA[

    physiofit4galaxy --galaxy

    #if $input_selection.input_selector == 'tsv':
        --data '$input_selection.datafile'
    #end if

    #if $input_selection.input_selector == 'json':
        --data '$input_selection.datafile'
        --config '$input_selection.cfgfile'
    #end if


    #if $basic_settings.lag:
        -l
    #end if

    #if $basic_settings.deg_select.deg == 'Yes':
        -d '$basic_settings.deg_select.degconsts'
    #end if

    #if $basic_settings.mc_select.montecarlo == 'Yes':
        -mc '$basic_settings.mc_select.iters'
    #end if

    --vini '$advanced_settings.vini'

    #if $advanced_settings.sd_select.sd == 'Yes':
        -s '$advanced_settings.sd_select.stddevs'
    #end if

    #if $advanced_settings.cm_select.cm == 'Yes':
        -cm '$advanced_settings.cm_select.conc_met_bounds'
    #end if

    #if $advanced_settings.fm_select.fm == 'Yes':
        -fm '$advanced_settings.fm_select.flux_met_bounds'
    #end if

    #if $advanced_settings.cb_select.cb == 'Yes':
        -cb '$advanced_settings.cb_select.conc_biom_bounds'
    #end if

    #if $advanced_settings.fb_select.fb == 'Yes':
        -fb '$advanced_settings.fb_select.flux_biom_bounds'
    #end if

    #if $advanced_settings.verbose:
        -v
    #end if

    -op '$plots' -of '$fluxes' -os '$stats' -oc '$config' 2> $log

    ]]></command>
    <inputs>

        <conditional name='input_selection'>
            <param name='input_selector' type='select' label='Choose the input data type to upload (tsv or json config file. For more information please check the documentation'>
                <option value='tsv'>tsv file</option>
                <option value='json'>config file (json)</option>
            </param>
            <when value='tsv'>
                <param name='datafile' type='data' format='tabular, txt' multiple='true' label='Upload data file containing biomass and concentration values'/>
            </when>
            <when value='json'>
                <param name='datafile' type='data' format='tabular, txt' multiple='true' label='Upload data file containing biomass and concentration values'/>
                <param name='cfgfile' type='data' format='json' label='Upload configuration file' />
            </when>
        </conditional>


        <section name='basic_settings' title='Basic Settings'>

            <param name='lag' type='boolean' argument='--lag' truevalue='-l' falsevalue='' label='Flag to estimate lag phase'/>

            <conditional name='deg_select'>
                <param name='deg' type='select' label='Select yes to add degradation constants'>
                    <option value='No'>No</option>
                    <option value='Yes'>Yes</option>
                </param>
                <when value='Yes'>
                    <param type='text' name='degconsts' value='{}' label='Enter degradation constants in dictionary format (see docs for more information)'>
                        <sanitizer>
                            <valid>
                                <add value='"'/>
                                <add value='{'/>
                                <add value='}'/>
                            </valid>
                        </sanitizer>
                    </param>
                </when>
            </conditional>

            <conditional name='mc_select'>
                <param name='montecarlo' type='select' label='Select yes for sensitivity analysis'>
                    <option value='Yes'>Yes</option>
                    <option value='No'>No</option>
                </param>
                <when value='Yes'>
                    <param name='iters' type='integer' value='100' label='Number of iterations for sensitivity analysis'/>
                </when>
            </conditional>

        </section>


        <section name='advanced_settings' title='Advanced Settings'>

            <param name='vini' type='float' value='1' label='Initial value for fluxes to estimate' />

            <conditional name='sd_select'>
                <param name='sd' type='select' label='Select yes to add standard deviations'>
                    <option value='No'>No</option>
                    <option value='Yes'>Yes</option>
                </param>
                <when value='Yes'>
                    <param name='stddevs' type='text' value='{}' label='Standard deviation on measurements. Give SDs in dictionary format (see docs for more information)'>
                        <sanitizer>
                            <valid>
                                <add value='"'/>
                                <add value='{'/>
                                <add value='}'/>
                            </valid>
                        </sanitizer>
                    </param>
                </when>
            </conditional>

            <conditional name='cm_select'>
                <param name='cm' type='select' label='Flag to add bounds on metabolite concentrations'>
                    <option value='No'>No</option>
                    <option value='Yes'>Yes</option>
                </param>
                <when value='Yes'>
                    <param name='conc_met_bounds' type='text' value='()' label='Bounds on metabolite concentrations. Bounds should be given in tuple format (see docs for more information)'/>

                </when>
            </conditional>

            <conditional name='fm_select'>
                <param name='fm' type='select' label='Select yes to add bounds on metabolite fluxes'>
                    <option value='No'>No</option>
                    <option value='Yes'>Yes</option>
                </param>
                <when value='Yes'>
                    <param name='flux_met_bounds' type='text' value='()' label='Bounds on metabolite fluxes. Bounds should be given in tuple format (see docs for more information)' />
                </when>
            </conditional>

            <conditional name='cb_select'>
                <param name='cb' type='select' label='Select yes to add bounds on biomass concentrations'>
                    <option value='No'>No</option>
                    <option value='Yes'>Yes</option>
                </param>
                <when value='Yes'>
                    <param name='conc_biom_bounds' type='text' value='()' label='Bounds on biomass concentrations. Bounds should be given in tuple format (see docs for more information)' />
                </when>
            </conditional>

            <conditional name='fb_select'>
                <param name='fb' type='select' label='Select yes to add bounds on biomass fluxes'>
                    <option value='No'>No</option>
                    <option value='Yes'>Yes</option>
                </param>
                <when value='Yes'>
                    <param name='flux_biom_bounds' type='text' value='()' label='Bounds on biomass fluxes. Bounds should be given in tuple format (see docs for more information)' />
                </when>
            </conditional>

            <param name='verbose' type='boolean' argument='--verbose' truevalue='-v' falsevalue='' label='Flag to get debug information'/>

        </section>

    </inputs>

    <outputs>
    <data name='plots' label='Plots' format='pdf'/>
    <data name='fluxes' label='Flux_results' format='tabular'/>
    <data name='stats' label='Stat_results' format='tabular'/>
    <data name='config' label='Config_file' format='json'/>
    <data name='log' label='Run_Log' format='txt'/>
    </outputs>

    <tests>
        <test>
            <param name='input_selection|input_selector' value='tsv' />
            <param name='input_selection|datafile' value='KEIO_ROBOT6_1.tsv' />
            <section name='basic_settings'>
                <param name='lag' value='No'/>
                <param name='deg_select|deg' value='No'/>
                <param name='mc_select|montecarlo' value='Yes'/>
            </section>
            <section name='advanced_settings'>
                <param name='vini' value='1'/>
                <param name='sd_select|sd' value='No'/>
                <param name='cm_select|cm' value='No'/>
                <param name='fm_select|fm' value='No'/>
                <param name='cb_select|cb' value='No'/>
                <param name='fb_select|fb' value='No'/>
                <param name='verbose' value='No'/>
            </section>
            <output name='fluxes'>
                <assert_contents>
                    <has_n_columns n='7'/>
                    <has_n_lines n='7'/>
                    <has_size value='767' delta='20'/>
                </assert_contents>
            </output>
        </test>
<!--        <test>-->
<!--            <param name='input_selection|input_selector' value='tsv' />-->
<!--            <param name='input_selection|datafile' value='KEIO_ROBOT6_1.tsv' />-->
<!--            <section name='basic_settings'>-->
<!--                <param name='lag' value='No'/>-->
<!--                <param name='deg_select|deg' value='No'/>-->
<!--                <param name='mc_select|montecarlo' value='No'/>-->
<!--            </section>-->
<!--            <section name='advanced_settings'>-->
<!--                <param name='vini' value='1'/>-->
<!--                <param name='sd_select|sd' value='No'/>-->
<!--                <param name='cm_select|cm' value='No'/>-->
<!--                <param name='fm_select|fm' value='No'/>-->
<!--                <param name='cb_select|cb' value='No'/>-->
<!--                <param name='fb_select|fb' value='No'/>-->
<!--                <param name='verbose' value='No'/>-->
<!--            </section>-->
<!--            <output name='fluxes' file='flux_results.tsv'/>-->
<!--        </test>-->
    </tests>

    <help><![CDATA[
.. class:: warningmark

**PhysioFit is a scientific tool designed to i) quantify exchange (production and consumption) fluxes and ii) cell growth
rate during (batch) cultivations of microorganisms.**

Fluxes are estimated from time-course measurements of extracellular metabolites and biomass concentrations. PhysioFit has been designed to
calculate fluxes in batch experiments, assuming cells are in metabolic (pseudo) steady-state (i.e. fluxes are constant during the experiment).

**PhysioFit includes the following features:**

   * **calculation of growth rate and extracellular (uptake and production) fluxes**.
   * if cell growth has some **lag** (e.g. due to adaptation to a novel environment), lag can be taken into account and lag time estimated.
   * **non-enzymatic degradation** of some metabolites (e.g. DHA or glutamine) can be estimated and taken into account when calculating fluxes.
   * sensitivity analyses are performed to **estimate the precision of the calculated fluxes**.
   * **evaluation of the goodness of fit and visual inspection of the fitted curves**.
   * shipped as a **library** with both a **graphical** and **command line** interface,
   * open-source, free and easy to install everywhere where Python 3 and pip run,
   * biologist-friendly.

It is one of the routine tools that we use at the MetaSys team and `MetaToul platform <http://www.metatoul.fr>`_ to calculate fluxes.

The code is open-source, and available on `GitHub <https://github.com/MetaSys-LISBP/PhysioFit/>`_ under a GPLv3 license.

We strongly encourage you to read the `documentation <https://physiofit.readthedocs.io/en/latest/>`_ before using PhysioFit.

    ]]></help>
    <citations>
        <citation type='bibtex'>
    @misc{githubphysiofit,
      author = {Le Gregam, Loic},
      year = {2022},
      title = {PhysioFit},
      publisher = {Peiro et al.},
      journal = {Appl Environ Microbiol},
      url = {https://journals.asm.org/doi/10.1128/AEM.00768-19},
    }</citation>
        </citations>
</tool>

2:232ad69fc93c

<tool id='physiofit' name='PhysioFit: extracellular flux calculation' version='@TOOL_VERSION@+galaxy0' python_template_version='3.5' profile='21.05'>
    <description>PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake and production fluxes</description>
    <macros>
        <token name='@TOOL_VERSION@'>3.3.2</token>
    </macros>
    <requirements>
        <requirement type='package' version='@TOOL_VERSION@'>physiofit</requirement>
    </requirements>
    <command detect_errors='exit_code'><![CDATA[
    physiofit
    --galaxy 
    --config $configfile 
    --data $datafile 
    -or '$recap' 
    -oz $zip 
    2> $log 
    ]]>
    </command>
    <inputs>
        <param name='datafile' type='data' format='tabular, txt' multiple='true' label='Upload data file containing biomass and concentration values'/>
        <param name='configfile' type='data' format='yaml' multiple='true' label='Upload yaml configuration file containing run parameters'/>
    </inputs>
    <outputs>
        <data name='recap' label='Summary file' format='csv'/>
        <data name='zip' label='Results' format='zip'/>
        <data name='log' label='Log' format='txt'/>
    </outputs>
    <tests>
        <test>
            <param name='datafile' value='data.txt'/>
            <param name='configfile' value='config_file.yml'/>
            <output name='recap'>
                <assert_contents>
                    <has_text text='experiments'/>
                    <has_text text='growth_rate'/>
                    <has_text text='Glc_q'/>
                    <has_text text='Glc_M0'/>
                    <has_text text='Ace_q'/>
                    <has_text text='Ace_M0'/>
                    <has_text text='optimal'/>
                    <has_text text='mean'/>
                </assert_contents>
            </output>
            <output name='zip'>
                <assert_contents>
                    <has_archive_member path='.*\.svg' min='3'/>
                    <has_archive_member path='.*\.tsv' min='2'/>
                    <has_archive_member path='.*\.pdf' min='1'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        **PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes**
    
        Fluxes are estimated using mathematical models by fitting time-course measurements of the concentration of
        cells and extracellular substrates and products. PhysioFit is shipped with some common growth models, and
        additional tailor-made models can be implemented by users.
        
        **PhysioFit includes the following features:**
        
            * **calculation of growth rate and extracellular (uptake and production) fluxes**,
            * **a set of steady-state and dynamic models** are shipped with PhysioFit,
            * **tailor-made models** can be constructed by users,
            * Monte-Carlo sensitivity analysis to **estimate the precision of the calculated fluxes**,
            * **evaluation of the goodness of fit and visual inspection of the fitted curves**,
            * shipped as a **library** with both a **graphical** and a **command line** interface,
            * **open-source, free and easy to install** everywhere where Python 3 and pip run,
            * **biologist-friendly**.
        
        It is one of the routine tools that we use at the
        `MetaSys team <https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-metasys/>`_
        and `MetaToul platform <https://mth-metatoul.com/>`_ to calculate fluxes.
        
        The code is open-source, and available on `GitHub <https://github.com/MetaSys-LISBP/PhysioFit/>`_ under a GPLv3 license.
        
        This documentation is available on Read the Docs (`https://physiofit.readthedocs.io <https://physiofit.readthedocs.io/>`_)
        and can be downloaded as a `PDF file <https://readthedocs.org/projects/physiofit/downloads/pdf/latest/>`_.
        
]]></help>
    <citations>
        <citation type='bibtex'>@article{10.1101/2023.10.12.561695,
            author = {Le Grégam, Loïc and Guitton, Yann and Bellvert, Floriant and Heux, Stéphanie and Jourdan, Fabien and Portais, Jean-Charles and Millard, Pierre},
            title = "{Physiofit: a software to quantify cell growth parameters and extracellular fluxes}",
            year = {2023},
            month = {10},
            abstract = '{Quantification of growth parameters and extracellular uptake and production fluxes is central in systems and synthetic biology. 
                Fluxes can be estimated using various mathematical models by fitting time-course measurements of the concentration of cells and 
                extracellular substrates and products. A single tool is available to calculate extracellular fluxes, but it is hardly interoperable and 
                includes a single hard-coded growth model. We present our open-source flux calculation software, PhysioFit, which can be used with any 
                growth model and is interoperable by design. PhysioFit includes by default the most common growth models, and additional models can be 
                implemented by users to calculate fluxes and other growth parameters for metabolic systems or experimental setups that follow alternative 
                kinetics. PhysioFit can be used as a Python library and includes a graphical user interface for intuitive use by end-users and a 
                command-line interface to streamline integration into existing pipelines.}',
            doi = {10.1101/2023.10.12.561695},
            url = {https://doi.org/10.1101/2023.10.12.561695},
        }
        </citation>
    </citations>
</tool>