| Previous changeset 1:52dddad92226 (2022-11-16) Next changeset 3:4e885e541368 (2024-03-13) |
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Commit message:
planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 79951a0ab2644ba8ca6615200e9be1a8645d78d4 |
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modified:
physiofit.xml |
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added:
test-data/config_file.yml test-data/data.txt test-data/output.csv test-data/output_zip.zip |
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removed:
test-data/KEIO_ROBOT6_1.tsv test-data/flux_results.tsv |
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| diff -r 52dddad92226 -r 232ad69fc93c physiofit.xml --- a/physiofit.xml Wed Nov 16 17:16:06 2022 +0000 +++ b/physiofit.xml Tue Jan 16 15:42:03 2024 +0000 |
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| b'@@ -1,278 +1,100 @@\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+<tool id=\'physiofit\' name=\'PhysioFit: extracellular flux calculation\' version=\'@TOOL_VERSION@+galaxy0\' python_template_version=\'3.5\' profile=\'21.05\'>\n+ <description>PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake and production fluxes</description>\n <macros>\n- <token name="@TOOL_VERSION@">2.2.1</token>\n+ <token name=\'@TOOL_VERSION@\'>3.3.2</token>\n </macros>\n <requirements>\n- <requirement type=\'package\' version=\'@TOOL_VERSION@\'>physiofit4galaxy</requirement>\n+ <requirement type=\'package\' version=\'@TOOL_VERSION@\'>physiofit</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_settings.deg_select.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\' 2> $log\n-\n- ]]></command>\n+ physiofit\n+ --galaxy \n+ --config $configfile \n+ --data $datafile \n+ -or \'$recap\' \n+ -oz $zip \n+ 2> $log \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'..b'Fit.\n-\n- ]]></help>\n+ **PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes**\n+ \n+ Fluxes are estimated using mathematical models by fitting time-course measurements of the concentration of\n+ cells and extracellular substrates and products. PhysioFit is shipped with some common growth models, and\n+ additional tailor-made models can be implemented by users.\n+ \n+ **PhysioFit includes the following features:**\n+ \n+ * **calculation of growth rate and extracellular (uptake and production) fluxes**,\n+ * **a set of steady-state and dynamic models** are shipped with PhysioFit,\n+ * **tailor-made models** can be constructed by users,\n+ * Monte-Carlo sensitivity analysis 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 a **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\n+ `MetaSys team <https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-metasys/>`_\n+ and `MetaToul platform <https://mth-metatoul.com/>`_ 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+ This documentation is available on Read the Docs (`https://physiofit.readthedocs.io <https://physiofit.readthedocs.io/>`_)\n+ and can be downloaded as a `PDF file <https://readthedocs.org/projects/physiofit/downloads/pdf/latest/>`_.\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+ <citation type=\'bibtex\'>@article{10.1101/2023.10.12.561695,\n+ author = {Le Gr\xc3\xa9gam, Lo\xc3\xafc and Guitton, Yann and Bellvert, Floriant and Heux, St\xc3\xa9phanie and Jourdan, Fabien and Portais, Jean-Charles and Millard, Pierre},\n+ title = "{Physiofit: a software to quantify cell growth parameters and extracellular fluxes}",\n+ year = {2023},\n+ month = {10},\n+ abstract = \'{Quantification of growth parameters and extracellular uptake and production fluxes is central in systems and synthetic biology. \n+ Fluxes can be estimated using various mathematical models by fitting time-course measurements of the concentration of cells and \n+ extracellular substrates and products. A single tool is available to calculate extracellular fluxes, but it is hardly interoperable and \n+ includes a single hard-coded growth model. We present our open-source flux calculation software, PhysioFit, which can be used with any \n+ growth model and is interoperable by design. PhysioFit includes by default the most common growth models, and additional models can be \n+ implemented by users to calculate fluxes and other growth parameters for metabolic systems or experimental setups that follow alternative \n+ kinetics. PhysioFit can be used as a Python library and includes a graphical user interface for intuitive use by end-users and a \n+ command-line interface to streamline integration into existing pipelines.}\',\n+ doi = {10.1101/2023.10.12.561695},\n+ url = {https://doi.org/10.1101/2023.10.12.561695},\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 52dddad92226 -r 232ad69fc93c test-data/KEIO_ROBOT6_1.tsv --- a/test-data/KEIO_ROBOT6_1.tsv Wed Nov 16 17:16:06 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,17 +0,0 @@ -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 52dddad92226 -r 232ad69fc93c test-data/config_file.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config_file.yml Tue Jan 16 15:42:03 2024 +0000 |
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| @@ -0,0 +1,23 @@ +iterations: 100 +mc: true +model: + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\millard\Documents\GIT\PhysioFit\data_test\Steady-state_model\data.txt +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 |
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| diff -r 52dddad92226 -r 232ad69fc93c test-data/data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data.txt Tue Jan 16 15:42:03 2024 +0000 |
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| @@ -0,0 +1,14 @@ +experiments time X Glc Ace +A 0 0.033264 NA NA +A 1.18888889 0.051408 NA NA +A 2.27694444 0.074088 NA NA +A 3.12833333 0.108864 NA NA +A 3.77138889 0.139104 NA NA +A 4.41555556 0.175392 NA NA +A 4.82277778 0.228312 NA NA +A 0.06666667 NA 15.81315 0.009505775 +A 1.71666667 NA 15.6035 0.294995312 +A 2.8 NA 13.76795 0.610747733 +A 3.63333333 NA 13.12348 0.997928907 +A 4.26666667 NA 12.69779 1.377281918 +A 4.88333333 NA 11.58289 1.804833542 |
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| diff -r 52dddad92226 -r 232ad69fc93c test-data/flux_results.tsv --- a/test-data/flux_results.tsv Wed Nov 16 17:16:06 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ - optimal mean sd median CI_2.5 CI_97.5 -X_0 0.030057356085279038 0.031020693652716442 0.01248214419475165 0.029507198033154346 0.011641988888053973 0.058342137145944405 -mu 0.5582759125316301 0.5686092117011008 0.08528431418544957 0.5617732771700231 0.4274326438805963 0.7428252946602405 -Glc_q -6.4690012286708845 -6.591939336986598 0.9573465913461194 -6.424216065589273 -8.689007040053548 -5.0804721629347975 -Glc_M0 14.102913181701245 14.093239782222746 0.3546457036884282 14.067487732809713 13.440594995883767 14.729084422532983 -Ace_q 2.4965870596545154 2.476648498253909 0.498894590813266 2.4157877116089033 1.7499997734065047 3.472079451670515 -Ace_M0 0.17844344816654867 0.20546717227239447 0.1953912180223188 0.17549120518463776 1e-06 0.7122213079215097 |
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| diff -r 52dddad92226 -r 232ad69fc93c test-data/output.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.csv Tue Jan 16 15:42:03 2024 +0000 |
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| @@ -0,0 +1,7 @@ +experiments,parameter name,optimal,mean,sd,median,CI_2.5,CI_97.5 +A,X_0,0.031416046332836525,0.03182035444450761,0.005889446987390569,0.03142333650054849,0.02023327944287703,0.04332078203780423 +A,growth_rate,0.4006864459114259,0.40211131871783157,0.04429485269871631,0.40086534734771084,0.32931826537615494,0.49089693037133325 +A,Glc_q,-9.180022678150166,-9.133793078913406,1.0337255786927726,-8.931030226348817,-11.239908883027535,-7.284934929582838 +A,Glc_M0,15.801477563634192,15.803710474829554,0.22508207962463989,15.808337292505701,15.385041267489758,16.222121607839906 +A,Ace_q,3.8199601365677696,3.7419073047720337,0.39020454597179627,3.7095971504962546,3.0629124776324934,4.595036468507531 +A,Ace_M0,0.0017301878123572975,0.03444074046224758,0.05451955290753988,1e-06,1e-06,0.16366853757506963 |
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| diff -r 52dddad92226 -r 232ad69fc93c test-data/output_zip.zip |
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| Binary file test-data/output_zip.zip has changed |