diff README.rst @ 2:57f199aa07e4 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911

--- a/README.rst	Wed Sep 13 19:52:44 2023 +0000
+++ b/README.rst	Wed Dec 13 08:56:04 2023 +0000
@@ -2,19 +2,22 @@
 Metabolic flux estimation
 -------------------------
 
-`influx_si` can be used for metabolic flux estimation based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). Tha name `influx_si` is used as common for both tools.
+`influx_si` can be used for estimation of metabolic fluxes and concentrations   based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). The name `influx_si` is used as common for both tools.
 
-The input for `influx_si` in one or several FTBL files, each describing a given labeling experiment and options to use during estimation. In addition, for `influx_i` a file with time course data has to be provided for each FTBL file.
+The input for `influx_si` is an MTF (Multiple TSV Files) collection describing metabolic network, label transition, labeling data and options to use during estimation.
+
+The output is a zip archive with files generated by `influx_si`. File ending with `.tvar.sim` which contains the estimated fluxes and concentrations. Other files ending with `.sim` contain simulated measurements. File ending with `.stat` has results of chi2 test assessing quality of fit.
 
-The output is a zip archive with files generated by `influx_si`. Among the most important is file ending with `_res.kvh` which contains the main information about estimated parameters, their statistics and so on.
-If, in your FTBL file, you have requested ploting information, it can be found in respective .pdf file.
+If, in your `.opt` file, you have requested plotting information (`plot_smeas.R` or `plot_ilab.R`), it can be found in the respective `.pdf` file.
+
+For detailed documentation about `influx_si` and accompanying tools see https://influx-si.readthedocs.io
 
-For detailed documentation about `influx_si` and accompanying tools see https://metasys.insa-toulouse.fr/software/influx/doc/
+For getting a standalone version of `influx_si <https://anaconda.org/bioconda/influx_si>`_, you can install it e.g. with `conda <https://docs.conda.io/en/latest/miniconda.html>`_ package manager: ::
 
-For getting a standalone version of `influx_si` see https://metasys.insa-toulouse.fr/software/influx/
+ conda install -c conda-forge -c bioconda influx_si
 
 Author: Serguei Sokol
 
 License: GPL2
 
-© INRAE 2020
+© INRAE/INSA/CNRS 2023