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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
author lecorguille
date Mon, 25 Apr 2016 11:15:29 -0400
parents df7b3b846cb6
children
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6:ca7c9a6da2c6 7:ed8d80fc927c
14 <BODY> 14 <BODY>
15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1> 15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
16 </div> 16 </div>
17 <h2>Samples used:</h2> 17 <h2>Samples used:</h2>
18 <div><table> 18 <div><table>
19 <tr><th>sample</th><th>filename</th></tr> 19 <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></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> 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>
21 </table> 21 </table>
22 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.
23 </div> 23 </div>
24 <h2>Function launched:</h2> 24 <h2>Function launched:</h2>
25 <div><table> 25 <div><table>
26 <tr><th>timestamp<sup>***</sup></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>
27 <tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td> 27 <tr><td rowspan='4'>160420-14:09:46</td><td rowspan='4'>xcmsSet</td>
28 <td>nSlaves</td><td>1</td></tr> 28 <td>nSlaves</td><td>1</td></tr>
29 <tr><td>method</td><td>matchedFilter</td></tr> 29 <tr><td>method</td><td>centWave</td></tr>
30 <tr><td>step</td><td>0.01</td></tr> 30 <tr><td>ppm</td><td>25</td></tr>
31 <tr><td>fwhm</td><td>30</td></tr> 31 <tr><td>peakwidth</td><td>2050</td></tr>
32 <tr><td rowspan='5'>151221-16:37:00</td><td rowspan='5'>group</td> 32 <tr><td rowspan='6'>160420-15:07:14</td><td rowspan='6'>group</td>
33 <td>method</td><td>density</td></tr> 33 <td>method</td><td>density</td></tr>
34 <tr><td>sleep</td><td>0.001</td></tr> 34 <tr><td>sleep</td><td>0.001</td></tr>
35 <tr><td>minfrac</td><td>0.5</td></tr> 35 <tr><td>minfrac</td><td>0.3</td></tr>
36 <tr><td>bw</td><td>30</td></tr> 36 <tr><td>bw</td><td>5</td></tr>
37 <tr><td>mzwid</td><td>0.25</td></tr> 37 <tr><td>mzwid</td><td>0.01</td></tr>
38 <tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td> 38 <tr><td>max</td><td>50</td></tr>
39 <tr><td rowspan='7'>160421-11:10:32</td><td rowspan='7'>retcor</td>
40 <td>method</td><td>peakgroups</td></tr>
41 <tr><td>smooth</td><td>loess</td></tr>
42 <tr><td>extra</td><td>1</td></tr>
43 <tr><td>missing</td><td>1</td></tr>
44 <tr><td>span</td><td>0.2</td></tr>
45 <tr><td>family</td><td>gaussian</td></tr>
46 <tr><td>plottype</td><td>deviation</td></tr>
47 <tr><td rowspan='6'>160421-11:19:31</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='1'>160421-11:50:48</td><td rowspan='1'>fillPeaks</td>
39 <td>method</td><td>chrom</td></tr> 55 <td>method</td><td>chrom</td></tr>
40 </table> 56 </table>
41 <br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss 57 <br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss
42 </div> 58 </div>
43 <h2>Informations about the xcmsSet object:</h2> 59 <h2>Informations about the xcmsSet object:</h2>
44 <div><pre> 60 <div><pre>
45 An "xcmsSet" object with 6 samples 61 An "xcmsSet" object with 4 samples
46 62
47 Time range: 16.3-1138.9 seconds (0.3-19 minutes) 63 Time range: 2506-4484 seconds (41.8-74.7 minutes)
48 Mass range: 61.9883-481.2446 m/z 64 Mass range: 200.1-600 m/z
49 Peaks: 1799 (about 300 per sample) 65 Peaks: 32720 (about 8180 per sample)
50 Peak Groups: 289 66 Peak Groups: 8157
51 Sample classes: bio, bio2, blank 67 Sample classes: KO, WT
52 68
53 Profile settings: method = bin 69 Profile settings: method = bin
54 step = 0.01 70 step = 0.1
55 71
56 Memory usage: 0.421 MB 72 Memory usage: 4.25 MB
57 </pre></div> 73 </pre></div>
58 <h2>Citations:</h2> 74 <h2>Citations:</h2>
59 <div><ul> 75 <div><ul>
60 <li>To cite the <b>XCMS</b> package in publications use: 76 <li>To cite the <b>XCMS</b> package in publications use:
61 <ul> 77 <ul>