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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
author lecorguille
date Fri, 08 Apr 2016 06:18:24 -0400
parents 8bc6408551e8
children 1ea35f88f3c4
comparison
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8:78fb71c535d0 9:dc6b3773f8de
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, tr, td, th { border: 1px solid #000000; border-collapse:collapse; } 7 table { min-width: 500px; border:1px solid #D6B161; border-collapse:collapse;}
8 td,th { padding: 5px; padding-right: 12px; } 8 th { background: #898989; text-align:left;}
9 th { background: #898989; text-align:left;color: white;} 9 tr { border: 1px solid #000000 }
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 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1> 15 <h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
16 </div>
17 <h2>Samples used:</h2> 16 <h2>Samples used:</h2>
18 <div><table> 17 <table
19 <tr><th>sample</th><th>filename</th></tr> 18 <tr><th>sample</th><th>filename</th></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> 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>
21 </table> 20 </table>
22
23 </div>
24 <h2>Function launched:</h2> 21 <h2>Function launched:</h2>
25 <div><table> 22 <table>
26 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr> 23 <tr><th>timestamp<br />(ymd-h:m:s)</th><th>function</th><th>argument</th><th>value</th></tr>
27 <tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td> 24 <tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td>
28 <td>nSlaves</td><td>1</td></tr> 25 <td>nSlaves</td><td>1</td></tr>
29 <tr><td>method</td><td>matchedFilter</td></tr> 26 <tr><td>method</td><td>matchedFilter</td></tr>
30 <tr><td>step</td><td>0.01</td></tr> 27 <tr><td>step</td><td>0.01</td></tr>
31 <tr><td>fwhm</td><td>30</td></tr> 28 <tr><td>fwhm</td><td>30</td></tr>
36 <tr><td>bw</td><td>30</td></tr> 33 <tr><td>bw</td><td>30</td></tr>
37 <tr><td>mzwid</td><td>0.25</td></tr> 34 <tr><td>mzwid</td><td>0.25</td></tr>
38 <tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td> 35 <tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td>
39 <td>method</td><td>chrom</td></tr> 36 <td>method</td><td>chrom</td></tr>
40 </table> 37 </table>
41 <br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss 38 <h2>Information about the xcmsSet object:</h2>
42 </div> 39 <pre>
43 <h2>Informations about the xcmsSet object:</h2>
44 <div><pre>
45 An "xcmsSet" object with 6 samples 40 An "xcmsSet" object with 6 samples
46 41
47 Time range: 16.3-1138.9 seconds (0.3-19 minutes) 42 Time range: 16.3-1138.9 seconds (0.3-19 minutes)
48 Mass range: 61.9883-481.2446 m/z 43 Mass range: 61.9883-481.2446 m/z
49 Peaks: 1799 (about 300 per sample) 44 Peaks: 1799 (about 300 per sample)
52 47
53 Profile settings: method = bin 48 Profile settings: method = bin
54 step = 0.01 49 step = 0.01
55 50
56 Memory usage: 0.421 MB 51 Memory usage: 0.421 MB
57 </pre></div> 52 </pre>
58 <h2>Citations:</h2> 53 <h2>Citations:</h2>
59 <div><ul> 54 <ul>
60 <li>To cite the <b>XCMS</b> package in publications use: 55 <li>To cite the <b>XCMS</b> package in publications use:
61 <ul> 56 <ul>
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> 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>
63 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li> 58 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</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> 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>
72 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use: 67 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
73 <ul> 68 <ul>
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> 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>
75 </ul> 70 </ul>
76 </li> 71 </li>
77 </ul></div> 72 </ul>
78 </BODY> 73 </BODY>
79 </HTML> 74 </HTML>