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changeset 5:df7b3b846cb6 draft

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planemo upload commit ac2bc76f498db6c51cb451b5e3a37640b35009fc-dirty
author lecorguille
date Fri, 18 Mar 2016 10:44:23 -0400
parents 42d621350901
children ca7c9a6da2c6
files abims_xcms_summary.xml test-data/report.html test-data/summary.html
diffstat 3 files changed, 80 insertions(+), 75 deletions(-) [+]
line wrap: on
line diff
--- a/abims_xcms_summary.xml	Thu Feb 25 09:00:20 2016 -0500
+++ b/abims_xcms_summary.xml	Fri Mar 18 10:44:23 2016 -0400
@@ -35,7 +35,7 @@
     <tests>
         <test>
             <param name="image" value="fillpeaks.RData" />
-            <output name="htmlOutput" file="summary.html" />
+            <output name="htmlOutput" file="summary.html" ftype="html" />
         </test>
     </tests>
     
--- a/test-data/report.html	Thu Feb 25 09:00:20 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-<!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 { min-width: 500px; border:1px solid #D6B161; border-collapse:collapse;}
-th { background: #898989; text-align:left;}
-tr { border: 1px solid #000000 }
-h2 { color: #FFA212; }
-ul li { margin-bottom:10px; }
-</style>
-</HEAD>
-<BODY>
-<h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
-<h2>Samples used:</h2>
-<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>
-<h2>Function launched:</h2>
-<table>
-<tr><th>timestamp<br />(ymd-h:m:s)</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>
-<h2>Information about the xcmsSet object:</h2>
-<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>
-<h2>Citations:</h2>
-<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>
-</BODY>
-</HTML>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summary.html	Fri Mar 18 10:44:23 2016 -0400
@@ -0,0 +1,79 @@
+<!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>