Mercurial > repos > ethevenot > profia
diff README.md @ 0:39ccace77270 draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
| author | ethevenot |
|---|---|
| date | Sun, 26 Mar 2017 17:37:12 -0400 |
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| children | 4753e64cf694 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sun Mar 26 17:37:12 2017 -0400 @@ -0,0 +1,62 @@ +Preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry data (FIA-HRMS) +=============================================================================================================== + +A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure + +Status: [](https://travis-ci.org/workflow4metabolomics/profia). + +### Description + +**Version:** 3.0.0 +**Date:** 2017-03-21 +**Author:** Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) +**Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) +**Citation:** Delabriere A., Hohenester U., Junot C. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. +**Licence:** CeCILL +**Reference history:** +**Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant) + +### Installation + +* Configuration file: `profia_config.xml` +* Image files: + + `static/images/profia_workflowPositionImage.png` + + `static/images/profia_workingExampleImage.png` +* Wrapper file: `profia_wrapper.R` +* R packages + + **batch** from CRAN + + ```r + install.packages("batch", dep=TRUE) + install.packages("FNN", dep=TRUE) + install.packages("maxLik", dep=TRUE) + install.packages("minpack.lm", dep=TRUE) + install.packages("pracma", dep=TRUE) + ``` + + **profia** from Bioconductor + + ```r + source("http://www.bioconductor.org/biocLite.R") + biocLite("xcms") + biocLite("proFIA") + biocLite("plasFIA") + ``` + +### Tests + +The code in the wrapper can be tested by running the `runit/profia_runtests.R` R file + +You will need to install **RUnit** package in order to make it run: +```r +install.packages('RUnit', dependencies = TRUE) +``` + +### Working example + +### News + +###### CHANGES IN VERSION 3.0.0 + +NEW FEATURE + + * Creation of the tool