Mercurial > repos > workflow4metabolomics > physiofit
changeset 0:198d81ccc75e draft
planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
| author | workflow4metabolomics |
|---|---|
| date | Fri, 28 Oct 2022 10:25:15 +0000 |
| parents | |
| children | 52dddad92226 |
| files | physiofit.xml test-data/KEIO_ROBOT6_1.tsv test-data/flux_results.tsv |
| diffstat | 3 files changed, 265 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/physiofit.xml Fri Oct 28 10:25:15 2022 +0000 @@ -0,0 +1,241 @@ +<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@">2.1.0</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_setting.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' + + ]]></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)'/> + </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)' /> + </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'/> + </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> + </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> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/KEIO_ROBOT6_1.tsv Fri Oct 28 10:25:15 2022 +0000 @@ -0,0 +1,17 @@ +time X Glc Ace +1.69472222222222 6.1992000000000005E-2 NA NA +2.3002777777777799 8.6184000000000011E-2 NA NA +2.6983333333333301 0.11037599999999999 NA NA +3.43611111111111 0.17841599999999999 NA NA +3.8211111111111098 0.20865600000000001 NA NA +4.2011111111111097 0.3024 NA NA +4.5980555555555496 0.378 NA NA +4.9950000000000001 0.54583199999999998 NA NA +5.3752777777777796 0.60933599999999999 NA NA +1.35 NA 13.6276813815462 0.216958848225059 +1.91666666666667 NA 13.5792133323062 0.371914222400848 +2.86666666666667 NA 12.6200457520069 0.707537683463011 +4 NA 11.2499817544224 1.46436775470691 +4.8 NA 9.36560347817446 2.13574936032777 +5.18333333333333 NA 8.20020915137498 2.54657962639804 +5.58333333333333 NA 6.55172432249331 2.88518116059672
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flux_results.tsv Fri Oct 28 10:25:15 2022 +0000 @@ -0,0 +1,7 @@ + optimal mean sd median CI_2.5 CI_97.5 +X_0 0.019837910042084236 0.020055047719088507 0.001936242015519126 0.020181433524903817 0.016385933648857588 0.023991705722000656 +mu 0.6448503161617235 0.6442401851491355 0.019838552319737378 0.6422759597671867 0.6055123753172559 0.6830180317435467 +Glc_q -6.7962941185743135 -6.774793454329362 0.39318776265927613 -6.801632529773193 -7.486259488979566 -6.0294828984301505 +Glc_M0 13.890941548678349 13.881503136428412 0.2268604387133866 13.89390411710686 13.42167220505119 14.364675598831429 +Ace_q 2.574083305172119 2.5516892907444007 0.34218910204223774 2.5706434692350855 1.8525815217489552 3.109731754802952 +Ace_M0 0.28632420734796105 0.28673563941751923 0.17207412150016024 0.2778487391600317 1e-06 0.6251737133158014