Mercurial > repos > ethevenot > profia
annotate README.md @ 1:4753e64cf694 draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
author | ethevenot |
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date | Wed, 03 May 2017 10:49:08 -0400 |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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1 Preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry data (FIA-HRMS) |
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2 =============================================================================================================== |
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3 |
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure |
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5 |
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6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/profia.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/profia). |
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7 |
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8 ### Description |
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9 |
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10 **Version:** 3.0.4 |
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11 **Date:** 2017-05-02 |
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12 **Author:** Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) |
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13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) |
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14 **Citation:** Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. |
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39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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15 **Licence:** CeCILL |
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16 **Reference history:** |
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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) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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18 |
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19 ### Installation |
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20 |
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21 * Configuration file: `profia_config.xml` |
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22 * Image files: |
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23 + `static/images/profia_workflowPositionImage.png` |
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24 + `static/images/profia_workingExampleImage.png` |
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25 * Wrapper file: `profia_wrapper.R` |
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26 * R packages |
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27 + **batch** from CRAN |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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28 |
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29 ```r |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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30 install.packages("batch", dep=TRUE) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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31 install.packages("FNN", dep=TRUE) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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32 install.packages("maxLik", dep=TRUE) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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33 install.packages("minpack.lm", dep=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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34 install.packages("pracma", dep=TRUE) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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35 ``` |
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36 + **profia** from Bioconductor |
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37 |
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38 ```r |
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39 source("http://www.bioconductor.org/biocLite.R") |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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40 biocLite("xcms") |
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4753e64cf694
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
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41 biocLite("plasFIA") |
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42 biocLite("proFIA") |
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43 ``` |
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44 |
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45 ### Tests |
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46 |
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47 The code in the wrapper can be tested by running the `runit/profia_runtests.R` R file |
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48 |
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49 You will need to install **RUnit** package in order to make it run: |
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50 ```r |
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51 install.packages('RUnit', dependencies = TRUE) |
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52 ``` |
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53 |
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54 ### Working example |
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55 |
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56 ### News |
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57 |
4753e64cf694
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58 ###### CHANGES IN VERSION 3.0.4 |
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59 |
4753e64cf694
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60 MINOR MODIFICATION |
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61 |
4753e64cf694
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62 * Details added in the documentation |
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63 |
4753e64cf694
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64 ###### CHANGES IN VERSION 3.0.2 |
4753e64cf694
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65 |
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66 NEW FEATURE |
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67 |
4753e64cf694
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68 * Parallel processing |
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69 |
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70 ###### CHANGES IN VERSION 3.0.0 |
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71 |
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72 NEW FEATURE |
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73 |
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74 * Creation of the tool |