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planemo upload commit ac2bc76f498db6c51cb451b5e3a37640b35009fc-dirty
author lecorguille
date Fri, 18 Mar 2016 10:44:23 -0400
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+<!DOCTYPE html>
+<HTML lang='en'>
+<HEAD>
+<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
+<title>[W4M] XCMS analysis summary</title>
+<style>
+table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }
+td,th { padding: 5px; padding-right: 12px; }
+th { background: #898989; text-align:left;color: white;}
+h2 { color: #FFA212; }
+ul li { margin-bottom:10px; }
+</style>
+</HEAD>
+<BODY>
+<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
+</div>
+<h2>Samples used:</h2>
+<div><table>
+<tr><th>sample</th><th>filename</th></tr>
+<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>
+</table>
+
+</div>
+<h2>Function launched:</h2>
+<div><table>
+<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
+<tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td>
+<td>nSlaves</td><td>1</td></tr>
+<tr><td>method</td><td>matchedFilter</td></tr>
+<tr><td>step</td><td>0.01</td></tr>
+<tr><td>fwhm</td><td>30</td></tr>
+<tr><td rowspan='5'>151221-16:37:00</td><td rowspan='5'>group</td>
+<td>method</td><td>density</td></tr>
+<tr><td>sleep</td><td>0.001</td></tr>
+<tr><td>minfrac</td><td>0.5</td></tr>
+<tr><td>bw</td><td>30</td></tr>
+<tr><td>mzwid</td><td>0.25</td></tr>
+<tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td>
+<td>method</td><td>chrom</td></tr>
+</table>
+<br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss
+</div>
+<h2>Informations about the xcmsSet object:</h2>
+<div><pre>
+An "xcmsSet" object with 6 samples
+
+Time range: 16.3-1138.9 seconds (0.3-19 minutes)
+Mass range: 61.9883-481.2446 m/z
+Peaks: 1799 (about 300 per sample)
+Peak Groups: 289 
+Sample classes: bio, bio2, blank 
+
+Profile settings: method = bin
+                  step = 0.01
+
+Memory usage: 0.421 MB
+</pre></div>
+<h2>Citations:</h2>
+<div><ul>
+<li>To cite the <b>XCMS</b> package in publications use:
+<ul>
+<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>
+<li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
+<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>
+</ul>
+</li>
+<li>To cite the <b>CAMERA</b> package in publications use:
+<ul>
+<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>
+</ul>
+</li>
+<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
+<ul>
+<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>
+</ul>
+</li>
+</ul></div>
+</BODY>
+</HTML>