# HG changeset patch
# User lecorguille
# Date 1458678067 14400
# Node ID 0692b03eeddc425cc807658f3375028a09700430
# Parent fdc068daa4a85ab862910df8ebd95a3b9b5cd9a7
planemo upload commit ac2bc76f498db6c51cb451b5e3a37640b35009fc-dirty
diff -r fdc068daa4a8 -r 0692b03eeddc abims_xcms_summary.xml
--- a/abims_xcms_summary.xml Sat Feb 20 05:15:38 2016 -0500
+++ b/abims_xcms_summary.xml Tue Mar 22 16:21:07 2016 -0400
@@ -34,8 +34,8 @@
-
-
+
+
diff -r fdc068daa4a8 -r 0692b03eeddc repository_dependencies.xml
--- a/repository_dependencies.xml Sat Feb 20 05:15:38 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-
-
-
-
-
diff -r fdc068daa4a8 -r 0692b03eeddc test-data/report.html
--- a/test-data/report.html Sat Feb 20 05:15:38 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
-
-
-
-
-
diff -r fdc068daa4a8 -r 0692b03eeddc test-data/summary.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summary.html Tue Mar 22 16:21:07 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
+
+
+
+
+
diff -r fdc068daa4a8 -r 0692b03eeddc xcms_summary.r
--- a/xcms_summary.r Sat Feb 20 05:15:38 2016 -0500
+++ b/xcms_summary.r Tue Mar 22 16:21:07 2016 -0400
@@ -139,7 +139,7 @@
writehtml("Informations about the CAMERA object:
")
writehtml("")
- writehtml("Number of pcgroup:",length(xa@pspectra))
+ writehtml("Number of pcgroup: ",length(xa@pspectra))
writehtml("
")
}
diff -r fdc068daa4a8 -r 0692b03eeddc xcms_summary.tgz
Binary file xcms_summary.tgz has changed