Mercurial > repos > workflow4metabolomics > influx_si

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
author workflow4metabolomics
date Wed, 13 Dec 2023 08:56:04 +0000
parents 9b03a930b08b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
1
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
2 Metabolic flux estimation
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
3 -------------------------
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
4
2
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
5 `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.
0
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
6
2
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
7 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.
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
8
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
9 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.
0
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
10
2
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
11 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.
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
12
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
13 For detailed documentation about `influx_si` and accompanying tools see https://influx-si.readthedocs.io
0
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
14
2
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
15 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: ::
0
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
16
2
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
17 conda install -c conda-forge -c bioconda influx_si
0
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
18
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
19 Author: Serguei Sokol
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
20
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
21 License: GPL2
9b03a930b08b "planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
workflow4metabolomics
parents:
diff changeset
22
2
57f199aa07e4 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
workflow4metabolomics
parents: 0
diff changeset
23 © INRAE/INSA/CNRS 2023