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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
author lecorguille
date Fri, 08 Apr 2016 10:33:40 -0400
parents dc6b3773f8de
children b302779347de
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2 <HTML lang='en'> 2 <HTML lang='en'>
3 <HEAD> 3 <HEAD>
4 <meta http-equiv='Content-Type' content='text/html; charset=UTF-8' /> 4 <meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
5 <title>[W4M] XCMS analysis summary</title> 5 <title>[W4M] XCMS analysis summary</title>
6 <style> 6 <style>
7 table { min-width: 500px; border:1px solid #D6B161; border-collapse:collapse;} 7 table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }
8 th { background: #898989; text-align:left;} 8 td,th { padding: 5px; padding-right: 12px; }
9 tr { border: 1px solid #000000 } 9 th { background: #898989; text-align:left;color: white;}
10 h2 { color: #FFA212; } 10 h2 { color: #FFA212; }
11 ul li { margin-bottom:10px; } 11 ul li { margin-bottom:10px; }
12 </style> 12 </style>
13 </HEAD> 13 </HEAD>
14 <BODY> 14 <BODY>
15 <h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1> 15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
16 </div>
16 <h2>Samples used:</h2> 17 <h2>Samples used:</h2>
17 <table 18 <div><table>
18 <tr><th>sample</th><th>filename</th></tr> 19 <tr><th>sample</th><th>filename</th></tr>
19 <tr><td> HU_neg_051 </td><td> sacuri//bio2/HU_neg_051.mzXML </td></tr><tr><td> HU_neg_060 </td><td> sacuri//bio2/HU_neg_060.mzXML </td></tr><tr><td> HU_neg_017 </td><td> sacuri//bio/HU_neg_017.mzXML </td></tr><tr><td> HU_neg_028 </td><td> sacuri//bio/HU_neg_028.mzXML </td></tr><tr><td> Blanc04 </td><td> sacuri//blank/Blanc04.mzXML </td></tr><tr><td> Blanc06 </td><td> sacuri//blank/Blanc06.mzXML </td></tr> 20 <tr> <td> HU_neg_051 </td> <td> sacuri//bio2/HU_neg_051.mzXML </td> </tr><tr> <td> HU_neg_060 </td> <td> sacuri//bio2/HU_neg_060.mzXML </td> </tr><tr> <td> HU_neg_017 </td> <td> sacuri//bio/HU_neg_017.mzXML </td> </tr><tr> <td> HU_neg_028 </td> <td> sacuri//bio/HU_neg_028.mzXML </td> </tr><tr> <td> Blanc04 </td> <td> sacuri//blank/Blanc04.mzXML </td> </tr><tr> <td> Blanc06 </td> <td> sacuri//blank/Blanc06.mzXML </td> </tr>
20 </table> 21 </table>
22
23 </div>
21 <h2>Function launched:</h2> 24 <h2>Function launched:</h2>
22 <table> 25 <div><table>
23 <tr><th>timestamp<br />(ymd-h:m:s)</th><th>function</th><th>argument</th><th>value</th></tr> 26 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
24 <tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td> 27 <tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td>
25 <td>nSlaves</td><td>1</td></tr> 28 <td>nSlaves</td><td>1</td></tr>
26 <tr><td>method</td><td>matchedFilter</td></tr> 29 <tr><td>method</td><td>matchedFilter</td></tr>
27 <tr><td>step</td><td>0.01</td></tr> 30 <tr><td>step</td><td>0.01</td></tr>
28 <tr><td>fwhm</td><td>30</td></tr> 31 <tr><td>fwhm</td><td>30</td></tr>
33 <tr><td>bw</td><td>30</td></tr> 36 <tr><td>bw</td><td>30</td></tr>
34 <tr><td>mzwid</td><td>0.25</td></tr> 37 <tr><td>mzwid</td><td>0.25</td></tr>
35 <tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td> 38 <tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td>
36 <td>method</td><td>chrom</td></tr> 39 <td>method</td><td>chrom</td></tr>
37 </table> 40 </table>
38 <h2>Information about the xcmsSet object:</h2> 41 <br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss
39 <pre> 42 </div>
43 <h2>Informations about the xcmsSet object:</h2>
44 <div><pre>
40 An "xcmsSet" object with 6 samples 45 An "xcmsSet" object with 6 samples
41 46
42 Time range: 16.3-1138.9 seconds (0.3-19 minutes) 47 Time range: 16.3-1138.9 seconds (0.3-19 minutes)
43 Mass range: 61.9883-481.2446 m/z 48 Mass range: 61.9883-481.2446 m/z
44 Peaks: 1799 (about 300 per sample) 49 Peaks: 1799 (about 300 per sample)
47 52
48 Profile settings: method = bin 53 Profile settings: method = bin
49 step = 0.01 54 step = 0.01
50 55
51 Memory usage: 0.421 MB 56 Memory usage: 0.421 MB
52 </pre> 57 </pre></div>
53 <h2>Citations:</h2> 58 <h2>Citations:</h2>
54 <ul> 59 <div><ul>
55 <li>To cite the <b>XCMS</b> package in publications use: 60 <li>To cite the <b>XCMS</b> package in publications use:
56 <ul> 61 <ul>
57 <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> 62 <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>
58 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li> 63 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
59 <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> 64 <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>
67 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use: 72 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
68 <ul> 73 <ul>
69 <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> 74 <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>
70 </ul> 75 </ul>
71 </li> 76 </li>
72 </ul> 77 </ul></div>
73 </BODY> 78 </BODY>
74 </HTML> 79 </HTML>