# HG changeset patch
# User lecorguille
# Date 1458312263 14400
# Node ID df7b3b846cb6b794735a032155fd75b7d834bde7
# Parent 42d621350901c77f79190924090ebf6f7a21177f
planemo upload commit ac2bc76f498db6c51cb451b5e3a37640b35009fc-dirty
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
@@ -35,7 +35,7 @@
-
+
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
@@ -1,74 +0,0 @@
-
-
-
-
-[W4M] XCMS analysis summary
-
-
-
-___ XCMS analysis summary using Workflow4Metabolomics ___
-Samples used:
-| sample | filename |
-| HU_neg_051 | sacuri//bio2/HU_neg_051.mzXML |
| HU_neg_060 | sacuri//bio2/HU_neg_060.mzXML |
| HU_neg_017 | sacuri//bio/HU_neg_017.mzXML |
| HU_neg_028 | sacuri//bio/HU_neg_028.mzXML |
| Blanc04 | sacuri//blank/Blanc04.mzXML |
| Blanc06 | sacuri//blank/Blanc06.mzXML |
-
-Function launched:
-
-timestamp
(ymd-h:m:s) | function | argument | value |
|---|
-| 151221-16:20:54 | xcmsSet |
-nSlaves | 1 |
-| method | matchedFilter |
-| step | 0.01 |
-| fwhm | 30 |
-| 151221-16:37:00 | group |
-method | density |
-| sleep | 0.001 |
-| minfrac | 0.5 |
-| bw | 30 |
-| mzwid | 0.25 |
-| 151221-16:37:20 | fillPeaks |
-method | chrom |
-
-Information about the xcmsSet object:
-
-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
-
-Citations:
-
-- To cite the XCMS package in publications use:
-
-- 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)
-- Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)
-- 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)
-
-
-- To cite the CAMERA package in publications use:
-
-- 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)
-
-
-- To cite the Workflow4Metabolimics (W4M) project in publications use:
-
-- 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
-
-
-
-
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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
@@ -0,0 +1,79 @@
+
+
+
+
+[W4M] XCMS analysis summary
+
+
+
+___ XCMS analysis summary using Workflow4Metabolomics ___
+
+Samples used:
+
+| sample | filename |
|---|
+ | HU_neg_051 | sacuri//bio2/HU_neg_051.mzXML |
| HU_neg_060 | sacuri//bio2/HU_neg_060.mzXML |
| HU_neg_017 | sacuri//bio/HU_neg_017.mzXML |
| HU_neg_028 | sacuri//bio/HU_neg_028.mzXML |
| Blanc04 | sacuri//blank/Blanc04.mzXML |
| Blanc06 | sacuri//blank/Blanc06.mzXML |
+
+
+
Function launched:
+
+| timestamp*** | function | argument | value |
|---|
+| 151221-16:20:54 | xcmsSet |
+nSlaves | 1 |
+| method | matchedFilter |
+| step | 0.01 |
+| fwhm | 30 |
+| 151221-16:37:00 | group |
+method | density |
+| sleep | 0.001 |
+| minfrac | 0.5 |
+| bw | 30 |
+| mzwid | 0.25 |
+| 151221-16:37:20 | fillPeaks |
+method | chrom |
+
+
***timestamp format: yymmdd-hh:mm:ss
+
Informations about the xcmsSet object:
+
+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
+
Citations:
+
+- To cite the XCMS package in publications use:
+
+- 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)
+- Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)
+- 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)
+
+
+- To cite the CAMERA package in publications use:
+
+- 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)
+
+
+- To cite the Workflow4Metabolimics (W4M) project in publications use:
+
+- 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
+
+
+