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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
author lecorguille
date Mon, 04 Jul 2016 08:47:02 -0400
parents ed8d80fc927c
children
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1 <!DOCTYPE html>
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2 <HTML lang='en'>
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3 <HEAD>
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4 <meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
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5 <title>[W4M] XCMS analysis summary</title>
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6 <style>
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7 table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }
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8 td,th { padding: 5px; padding-right: 12px; }
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9 th { background: #898989; text-align:left;color: white;}
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10 h2 { color: #FFA212; }
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11 ul li { margin-bottom:10px; }
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12 </style>
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13 </HEAD>
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14 <BODY>
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15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
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16 </div>
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17 <h2>Samples used:</h2>
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18 <div><table>
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19 <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr>
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20 <tr> <td> ko15 </td> <td> faahKO_reduce/KO/ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> faahKO_reduce/KO/ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> faahKO_reduce/WT/wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> faahKO_reduce/WT/wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr>
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21 </table>
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22 <br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process.
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23 </div>
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24 <h2>Function launched:</h2>
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25 <div><table>
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26 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
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27 <tr><td rowspan='4'>160420-14:09:46</td><td rowspan='4'>xcmsSet</td>
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28 <td>nSlaves</td><td>1</td></tr>
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29 <tr><td>method</td><td>centWave</td></tr>
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30 <tr><td>ppm</td><td>25</td></tr>
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31 <tr><td>peakwidth</td><td>2050</td></tr>
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32 <tr><td rowspan='6'>160420-15:07:14</td><td rowspan='6'>group</td>
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33 <td>method</td><td>density</td></tr>
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34 <tr><td>sleep</td><td>0.001</td></tr>
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35 <tr><td>minfrac</td><td>0.3</td></tr>
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36 <tr><td>bw</td><td>5</td></tr>
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37 <tr><td>mzwid</td><td>0.01</td></tr>
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38 <tr><td>max</td><td>50</td></tr>
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39 <tr><td rowspan='7'>160421-11:10:32</td><td rowspan='7'>retcor</td>
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40 <td>method</td><td>peakgroups</td></tr>
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41 <tr><td>smooth</td><td>loess</td></tr>
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42 <tr><td>extra</td><td>1</td></tr>
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43 <tr><td>missing</td><td>1</td></tr>
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44 <tr><td>span</td><td>0.2</td></tr>
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45 <tr><td>family</td><td>gaussian</td></tr>
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46 <tr><td>plottype</td><td>deviation</td></tr>
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47 <tr><td rowspan='6'>160421-11:19:31</td><td rowspan='6'>group</td>
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48 <td>method</td><td>density</td></tr>
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49 <tr><td>sleep</td><td>0.001</td></tr>
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50 <tr><td>minfrac</td><td>0.3</td></tr>
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51 <tr><td>bw</td><td>5</td></tr>
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52 <tr><td>mzwid</td><td>0.01</td></tr>
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53 <tr><td>max</td><td>50</td></tr>
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54 <tr><td rowspan='1'>160421-11:50:48</td><td rowspan='1'>fillPeaks</td>
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55 <td>method</td><td>chrom</td></tr>
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56 </table>
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57 <br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss
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58 </div>
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59 <h2>Informations about the xcmsSet object:</h2>
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60 <div><pre>
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61 An "xcmsSet" object with 4 samples
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62
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63 Time range: 2506-4484 seconds (41.8-74.7 minutes)
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64 Mass range: 200.1-600 m/z
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65 Peaks: 32720 (about 8180 per sample)
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66 Peak Groups: 8157
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67 Sample classes: KO, WT
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68
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69 Profile settings: method = bin
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70 step = 0.1
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71
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72 Memory usage: 4.25 MB
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73 </pre></div>
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74 <h2>Citations:</h2>
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75 <div><ul>
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76 <li>To cite the <b>XCMS</b> package in publications use:
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77 <ul>
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78 <li>Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)</li>
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79 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
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80 <li>H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)</li>
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81 </ul>
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82 </li>
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83 <li>To cite the <b>CAMERA</b> package in publications use:
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84 <ul>
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85 <li>Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)</li>
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86 </ul>
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87 </li>
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88 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
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89 <ul>
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90 <li>Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813</li>
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91 </ul>
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92 </li>
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93 </ul></div>
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94 </BODY>
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95 </HTML>