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comparison test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html @ 12:27e7da5f6848 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author lecorguille
date Fri, 07 Apr 2017 07:37:23 -0400
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11:cb599006715f 12:27e7da5f6848
1 <!DOCTYPE html>
2 <HTML lang='en'>
3 <HEAD>
4 <meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
5 <title>[W4M] XCMS analysis summary</title>
6 <style>
7 table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }
8 td,th { padding: 5px; padding-right: 12px; }
9 th { background: #898989; text-align:left;color: white;}
10 h2 { color: #FFA212; }
11 ul li { margin-bottom:10px; }
12 </style>
13 </HEAD>
14 <BODY>
15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
16 </div>
17 <h2>Samples used:</h2>
18 <div><table>
19 <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr>
20 <tr> <td> ko15 </td> <td> ./ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> ./ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> ./wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> ./wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr>
21 </table>
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 changed during the process.
23 </div>
24 <h2>Function launched:</h2>
25 <div><table>
26 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
27 <tr><td rowspan='4'>170203-11:04:42</td><td rowspan='4'>xcmsSet</td>
28 <td>nSlaves</td><td>1</td></tr>
29 <tr><td>method</td><td>centWave</td></tr>
30 <tr><td>ppm</td><td>25</td></tr>
31 <tr><td>peakwidth</td><td>2050</td></tr>
32 <tr><td rowspan='4'>170203-11:05:21</td><td rowspan='4'>xcmsSet</td>
33 <td>nSlaves</td><td>1</td></tr>
34 <tr><td>method</td><td>centWave</td></tr>
35 <tr><td>ppm</td><td>25</td></tr>
36 <tr><td>peakwidth</td><td>2050</td></tr>
37 <tr><td rowspan='4'>170203-11:06:21</td><td rowspan='4'>xcmsSet</td>
38 <td>nSlaves</td><td>1</td></tr>
39 <tr><td>method</td><td>centWave</td></tr>
40 <tr><td>ppm</td><td>25</td></tr>
41 <tr><td>peakwidth</td><td>2050</td></tr>
42 <tr><td rowspan='4'>170203-11:06:59</td><td rowspan='4'>xcmsSet</td>
43 <td>nSlaves</td><td>1</td></tr>
44 <tr><td>method</td><td>centWave</td></tr>
45 <tr><td>ppm</td><td>25</td></tr>
46 <tr><td>peakwidth</td><td>2050</td></tr>
47 <tr><td rowspan='6'>170203-14:38:53</td><td rowspan='6'>group</td>
48 <td>method</td><td>density</td></tr>
49 <tr><td>sleep</td><td>0.001</td></tr>
50 <tr><td>minfrac</td><td>0.3</td></tr>
51 <tr><td>bw</td><td>5</td></tr>
52 <tr><td>mzwid</td><td>0.01</td></tr>
53 <tr><td>max</td><td>50</td></tr>
54 <tr><td rowspan='7'>170203-14:51:16</td><td rowspan='7'>retcor</td>
55 <td>method</td><td>peakgroups</td></tr>
56 <tr><td>smooth</td><td>loess</td></tr>
57 <tr><td>extra</td><td>1</td></tr>
58 <tr><td>missing</td><td>1</td></tr>
59 <tr><td>span</td><td>0.2</td></tr>
60 <tr><td>family</td><td>gaussian</td></tr>
61 <tr><td>plottype</td><td>deviation</td></tr>
62 <tr><td rowspan='6'>170203-15:27:58</td><td rowspan='6'>group</td>
63 <td>method</td><td>density</td></tr>
64 <tr><td>sleep</td><td>0.001</td></tr>
65 <tr><td>minfrac</td><td>0.3</td></tr>
66 <tr><td>bw</td><td>5</td></tr>
67 <tr><td>mzwid</td><td>0.01</td></tr>
68 <tr><td>max</td><td>50</td></tr>
69 <tr><td rowspan='5'>170203-15:44:50</td><td rowspan='5'>fillPeaks</td>
70 <td>method</td><td>chrom</td></tr>
71 <tr><td>convertRTMinute</td><td>FALSE</td></tr>
72 <tr><td>numDigitsMZ</td><td>4</td></tr>
73 <tr><td>numDigitsRT</td><td>1</td></tr>
74 <tr><td>intval</td><td>into</td></tr>
75 </table>
76 <br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss
77 </div>
78 <h2>Informations about the xcmsSet object:</h2>
79 <div><pre>
80 An "xcmsSet" object with 4 samples
81
82 Time range: 2506-4484 seconds (41.8-74.7 minutes)
83 Mass range: 200.1-600 m/z
84 Peaks: 32720 (about 8180 per sample)
85 Peak Groups: 8157
86 Sample classes: KO, WT
87
88 Peak picking was performed on MS1.
89 Profile settings: method = bin
90 step = 0.1
91
92 Memory usage: 4.25 MB
93 </pre></div>
94 <h2>Citations:</h2>
95 <div><ul>
96 <li>To cite the <b>XCMS</b> package in publications use:
97 <ul>
98 <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>
99 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
100 <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>
101 </ul>
102 </li>
103 <li>To cite the <b>CAMERA</b> package in publications use:
104 <ul>
105 <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>
106 </ul>
107 </li>
108 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
109 <ul>
110 <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>
111 </ul>
112 </li>
113 </ul></div>
114 </BODY>
115 </HTML>