Mercurial > repos > ethevenot > profia
comparison README.md @ 0:39ccace77270 draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
author | ethevenot |
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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 |