| Next changeset 1:52dddad92226 (2022-11-16) |
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Commit message:
planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1 |
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added:
physiofit.xml test-data/KEIO_ROBOT6_1.tsv test-data/flux_results.tsv |
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| diff -r 000000000000 -r 198d81ccc75e physiofit.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/physiofit.xml Fri Oct 28 10:25:15 2022 +0000 |
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| b'@@ -0,0 +1,241 @@\n+<tool id=\'physiofit\' name=\'PhysioFit\' profile=\'21.09\' version=\'@TOOL_VERSION@+galaxy0\' python_template_version=\'3.5\'>\n+ <description>Extracellular flux analysis</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">2.1.0</token>\n+ </macros>\n+ <requirements>\n+ <requirement type=\'package\' version=\'@TOOL_VERSION@\'>physiofit4galaxy</requirement>\n+ </requirements>\n+ <command detect_errors=\'exit_code\'><![CDATA[\n+\n+ physiofit4galaxy --galaxy\n+\n+ #if $input_selection.input_selector == \'tsv\':\n+ --data \'$input_selection.datafile\'\n+ #end if\n+\n+ #if $input_selection.input_selector == \'json\':\n+ --data \'$input_selection.datafile\'\n+ --config \'$input_selection.cfgfile\'\n+ #end if\n+\n+\n+ #if $basic_settings.lag:\n+ -l\n+ #end if\n+\n+ #if $basic_settings.deg_select.deg == \'Yes\':\n+ -d \'$basic_setting.degconsts\'\n+ #end if\n+\n+ #if $basic_settings.mc_select.montecarlo == \'Yes\':\n+ -mc \'$basic_settings.mc_select.iters\'\n+ #end if\n+\n+ --vini \'$advanced_settings.vini\'\n+\n+ #if $advanced_settings.sd_select.sd == \'Yes\':\n+ -s \'$advanced_settings.sd_select.stddevs\'\n+ #end if\n+\n+ #if $advanced_settings.cm_select.cm == \'Yes\':\n+ -cm \'$advanced_settings.cm_select.conc_met_bounds\'\n+ #end if\n+\n+ #if $advanced_settings.fm_select.fm == \'Yes\':\n+ -fm \'$advanced_settings.fm_select.flux_met_bounds\'\n+ #end if\n+\n+ #if $advanced_settings.cb_select.cb == \'Yes\':\n+ -cb \'$advanced_settings.cb_select.conc_biom_bounds\'\n+ #end if\n+\n+ #if $advanced_settings.fb_select.fb == \'Yes\':\n+ -fb \'$advanced_settings.fb_select.flux_biom_bounds\'\n+ #end if\n+\n+ #if $advanced_settings.verbose:\n+ -v\n+ #end if\n+\n+ -op \'$plots\' -of \'$fluxes\' -os \'$stats\' -oc \'$config\'\n+\n+ ]]></command>\n+ <inputs>\n+\n+ <conditional name=\'input_selection\'>\n+ <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\'>\n+ <option value=\'tsv\'>tsv file</option>\n+ <option value=\'json\'>config file (json)</option>\n+ </param>\n+ <when value=\'tsv\'>\n+ <param name=\'datafile\' type=\'data\' format=\'tabular, txt\' multiple=\'true\' label=\'Upload data file containing biomass and concentration values\'/>\n+ </when>\n+ <when value=\'json\'>\n+ <param name=\'datafile\' type=\'data\' format=\'tabular, txt\' multiple=\'true\' label=\'Upload data file containing biomass and concentration values\'/>\n+ <param name=\'cfgfile\' type=\'data\' format=\'json\' label=\'Upload configuration file\' />\n+ </when>\n+ </conditional>\n+\n+\n+ <section name=\'basic_settings\' title=\'Basic Settings\'>\n+\n+ <param name=\'lag\' type=\'boolean\' argument=\'--lag\' truevalue=\'-l\' falsevalue=\'\' label=\'Flag to estimate lag phase\'/>\n+\n+ <conditional name=\'deg_select\'>\n+ <param name=\'deg\' type=\'select\' label=\'Select yes to add degradation constants\'>\n+ <option value=\'No\'>No</option>\n+ <option value=\'Yes\'>Yes</option>\n+ </param>\n+ <when value=\'Yes\'>\n+ <param type=\'text\' name=\'degconsts\' value=\'{}\' label=\'Enter degradation constants in dictionary format (see docs for more information)\'/>\n+ </when>\n+ </conditional>\n+\n+ <conditional name=\'mc_select\'>\n+ <param name=\'montecarlo\' type=\'select\' label=\'Select yes for sensitivity analysis\'>\n+ <option value=\'Yes\'>Yes</option>\n+ <option value=\'No\'>No</option>\n+ </param>\n+ <when value=\'Yes\'>\n+ <param name=\'iters\' type=\'integer\' value=\'100\' label=\'Number of iterations for sensitivity analysis\'/>\n+ </when>\n+ </condi'..b"Yes'>\n+ <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)' />\n+ </when>\n+ </conditional>\n+\n+ <param name='verbose' type='boolean' argument='--verbose' truevalue='-v' falsevalue='' label='Flag to get debug information'/>\n+\n+ </section>\n+\n+ </inputs>\n+\n+ <outputs>\n+ <data name='plots' label='Plots' format='pdf'/>\n+ <data name='fluxes' label='Flux_results' format='tabular'/>\n+ <data name='stats' label='Stat_results' format='tabular'/>\n+ <data name='config' label='Config_file' format='json'/>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name='input_selection|input_selector' value='tsv' />\n+ <param name='input_selection|datafile' value='KEIO_ROBOT6_1.tsv' />\n+ <section name='basic_settings'>\n+ <param name='lag' value='No'/>\n+ <param name='deg_select|deg' value='No'/>\n+ <param name='mc_select|montecarlo' value='Yes'/>\n+ </section>\n+ <section name='advanced_settings'>\n+ <param name='vini' value='1'/>\n+ <param name='sd_select|sd' value='No'/>\n+ <param name='cm_select|cm' value='No'/>\n+ <param name='fm_select|fm' value='No'/>\n+ <param name='cb_select|cb' value='No'/>\n+ <param name='fb_select|fb' value='No'/>\n+ <param name='verbose' value='No'/>\n+ </section>\n+ <output name='fluxes'>\n+ <assert_contents>\n+ <has_n_columns n='7'/>\n+ <has_n_lines n='7'/>\n+ <has_size value='767' delta='20'/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+.. class:: warningmark\n+\n+**PhysioFit is a scientific tool designed to i) quantify exchange (production and consumption) fluxes and ii) cell growth\n+rate during (batch) cultivations of microorganisms.**\n+\n+Fluxes are estimated from time-course measurements of extracellular metabolites and biomass concentrations. PhysioFit has been designed to\n+calculate fluxes in batch experiments, assuming cells are in metabolic (pseudo) steady-state (i.e. fluxes are constant during the experiment).\n+\n+**PhysioFit includes the following features:**\n+\n+ * **calculation of growth rate and extracellular (uptake and production) fluxes**.\n+ * 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.\n+ * **non-enzymatic degradation** of some metabolites (e.g. DHA or glutamine) can be estimated and taken into account when calculating fluxes.\n+ * sensitivity analyses are performed to **estimate the precision of the calculated fluxes**.\n+ * **evaluation of the goodness of fit and visual inspection of the fitted curves**.\n+ * shipped as a **library** with both a **graphical** and **command line** interface,\n+ * open-source, free and easy to install everywhere where Python 3 and pip run,\n+ * biologist-friendly.\n+\n+It is one of the routine tools that we use at the MetaSys team and `MetaToul platform <http://www.metatoul.fr>`_ to calculate fluxes.\n+\n+The code is open-source, and available on `GitHub <https://github.com/MetaSys-LISBP/PhysioFit/>`_ under a GPLv3 license.\n+\n+We strongly encourage you to read the `documentation <https://physiofit.readthedocs.io/en/latest/>`_ before using PhysioFit.\n+\n+ ]]></help>\n+ <citations>\n+ <citation type='bibtex'>\n+ @misc{githubphysiofit,\n+ author = {Le Gregam, Loic},\n+ year = {2022},\n+ title = {PhysioFit},\n+ publisher = {Peiro et al.},\n+ journal = {Appl Environ Microbiol},\n+ url = {https://journals.asm.org/doi/10.1128/AEM.00768-19},\n+ }</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n" |
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| diff -r 000000000000 -r 198d81ccc75e test-data/KEIO_ROBOT6_1.tsv --- /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 |
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| @@ -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 |
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| diff -r 000000000000 -r 198d81ccc75e test-data/flux_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flux_results.tsv Fri Oct 28 10:25:15 2022 +0000 |
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| @@ -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 |