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author ethevenot
date Sun, 26 Mar 2017 17:37:12 -0400
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1 Preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry data (FIA-HRMS)
2 ===============================================================================================================
3
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
5
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/profia.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/profia).
7
8 ### Description
9
10 **Version:** 3.0.0
11 **Date:** 2017-03-21
12 **Author:** Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
14 **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*.
15 **Licence:** CeCILL
16 **Reference history:**
17 **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)
18
19 ### Installation
20
21 * Configuration file: `profia_config.xml`
22 * Image files:
23 + `static/images/profia_workflowPositionImage.png`
24 + `static/images/profia_workingExampleImage.png`
25 * Wrapper file: `profia_wrapper.R`
26 * R packages
27 + **batch** from CRAN
28
29 ```r
30 install.packages("batch", dep=TRUE)
31 install.packages("FNN", dep=TRUE)
32 install.packages("maxLik", dep=TRUE)
33 install.packages("minpack.lm", dep=TRUE)
34 install.packages("pracma", dep=TRUE)
35 ```
36 + **profia** from Bioconductor
37
38 ```r
39 source("http://www.bioconductor.org/biocLite.R")
40 biocLite("xcms")
41 biocLite("proFIA")
42 biocLite("plasFIA")
43 ```
44
45 ### Tests
46
47 The code in the wrapper can be tested by running the `runit/profia_runtests.R` R file
48
49 You will need to install **RUnit** package in order to make it run:
50 ```r
51 install.packages('RUnit', dependencies = TRUE)
52 ```
53
54 ### Working example
55
56 ### News
57
58 ###### CHANGES IN VERSION 3.0.0
59
60 NEW FEATURE
61
62 * Creation of the tool