Mercurial > repos > ethevenot > qualitymetrics
annotate README.md @ 3:acdf51018708 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit b7e47e59ea753fe9f73f2b83bcaae895b21269f6
author | ethevenot |
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date | Wed, 28 Feb 2018 09:32:42 -0500 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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1 Metrics and graphics to assess the quality of the data |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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2 ====================================================== |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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3 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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5 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/qualitymetrics.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/qualitymetrics). |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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7 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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8 ### Description |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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9 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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10 **Version:** 2.2.8 |
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11 **Date:** 2018-01-11 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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12 **Author:** Marion Landi (INRA, PFEM), Mélanie Pétéra (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST) |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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13 **Email:** [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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14 **Citation:** |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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15 **Licence:** CeCILL |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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16 **Reference history:** [W4M00001b_sacurine-complete](http://galaxy.workflow4metabolomics.org/history/list_published) |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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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) |
b4f5b5bc01dd
planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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18 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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19 ### Installation |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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20 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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21 * Configuration file: |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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22 + `qualitymetrics_config.xml` |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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23 * Image files: |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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24 + `static/images/QualityControl.png` |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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25 + `static/images/qualitymetrics_workingExampleImage.png` |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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26 * Wrapper file: |
b4f5b5bc01dd
planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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27 + `qualitymetrics_wrapper.R` |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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28 * Script file: |
b4f5b5bc01dd
planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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29 + `qualitymetrics_script.R` |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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30 * R packages |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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31 + **batch** from CRAN |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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32 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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33 ```r |
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34 install.packages("batch", dep=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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35 ``` |
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36 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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37 + **ropls** from Bioconductor |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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38 |
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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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39 ```r |
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40 source("http://www.bioconductor.org/biocLite.R") |
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41 biocLite("ropls") |
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42 ``` |
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43 |
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44 ### Tests |
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45 |
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46 The code in the wrapper can be tested by running the `runit/qualitymetrics_runtests.R` R file |
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47 |
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48 You will need to install **RUnit** package in order to make it run: |
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49 ```r |
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50 install.packages('RUnit', dependencies = TRUE) |
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51 ``` |
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52 |
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53 ### News |
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54 |
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55 ##### CHANGES IN VERSION 2.2.8 |
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56 |
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57 MINOR MODIFICATION |
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58 |
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59 In the case of a distinct sample order between dataMatrix and sampleMetadata, the sample order from the dataMatrix is matched to sampleMetadata internally for the computations and graphics without modifying the order in the sampleMetadata output (a warning is generated in the information file); to get the re-ordered dataMatrix as output, please use the Check Format module |
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60 |
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61 ##### CHANGES IN VERSION 2.2.6 |
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62 |
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63 MINOR MODIFICATION |
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64 |
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65 * Graphic (pool_CV inferior to 30% metric): pools with a NaN value are now counted as having a value superior to 30% (to avoid generating a final NA metric value) |
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66 |
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67 ##### CHANGES IN VERSION 2.2.4 |
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68 |
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69 INTERNAL MODIFICATION |
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70 |
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71 * Additional running and installation tests added with planemo, conda, and travis |
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72 |
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73 ##### CHANGES IN VERSION 2.2.3 |
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74 |
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75 INTERNAL MODIFICATION |
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76 |
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77 * Modifications of the 'qualitymetrics_script.R' file to handle the recent 'ropls' package versions (i.e. 1.3.15 and above) which use S4 classes |
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78 |
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79 * Creating tests for the R code |
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80 |
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81 ##### CHANGES IN VERSION 2.2.2 |
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82 |
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83 INTERNAL MODIFICATION |
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84 |
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85 * Minor internal modification |