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Commit message:
planemo upload commit ac2bc76f498db6c51cb451b5e3a37640b35009fc-dirty |
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modified:
abims_xcms_summary.xml |
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added:
test-data/summary.html |
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removed:
test-data/report.html |
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| diff -r 42d621350901 -r df7b3b846cb6 abims_xcms_summary.xml --- 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 |
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| @@ -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> |
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| diff -r 42d621350901 -r df7b3b846cb6 test-data/report.html --- a/test-data/report.html Thu Feb 25 09:00:20 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |
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| diff -r 42d621350901 -r df7b3b846cb6 test-data/summary.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary.html Fri Mar 18 10:44:23 2016 -0400 |
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| @@ -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> |