# HG changeset patch # User lecorguille # Date 1455899526 18000 # Node ID 768a8069bb8f935032768660652f96899feadc04 # Parent 6260844b9a17f073e33a10167f372536acadb57b Uploaded diff -r 6260844b9a17 -r 768a8069bb8f Makefile --- a/Makefile Fri Feb 19 11:00:57 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -# USAGE: make [install|clean] - -# -------- VARIABLE -------- - -OBJ=xcms_summary.tgz -DEP=abims_xcms_summary.xml xcms_summary.r tool_dependencies.xml repository_dependencies.xml test-data - - -# ------------------------ - -all: $(OBJ) - -$(OBJ): $(DEP) - tar --exclude=".svn" -zchf $@ $^ - -# ------------------------ - -install: $(OBJ) - mv *.tgz ~ - -clean: - rm *.tgz - diff -r 6260844b9a17 -r 768a8069bb8f README.rst --- a/README.rst Fri Feb 19 11:00:57 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ - -Changelog/News --------------- - -**Version 1.0.0 - 10/02/2016** - -- NEW: Create a summary of XCMS analysis - diff -r 6260844b9a17 -r 768a8069bb8f planemo.sh --- a/planemo.sh Fri Feb 19 11:00:57 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -planemo shed_init -f --name=xcms_summary --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS analysis" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nThis tool create a HTML summary of XCMS analysis" --category="Metabolomics" diff -r 6260844b9a17 -r 768a8069bb8f test-data/.svn/entries --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/entries Fri Feb 19 11:32:06 2016 -0500 @@ -0,0 +1,96 @@ +10 + +dir +234 +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_summary/test-data +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo + + + +2016-02-19T15:58:48.218379Z +234 +lecorguille + + + + + + + + + + + + + + +87d02074-be8c-4456-a071-04b64888326c + +fillpeaks.RData +file + + + + +2016-02-19T15:55:14.364130Z +ad9e3cfef6c684bc4203efb101445274 +2016-02-19T15:58:48.218379Z +234 +lecorguille +has-props + + + + + + + + + + + + + + + + + + + + +178113 + +report.html +file + + + + +2016-02-19T15:55:14.364130Z +f1b08eb3da7992bd6627032dcc82362a +2016-02-19T15:58:48.218379Z +234 +lecorguille + + + + + + + + + + + + + + + + + + + + + +3572 + diff -r 6260844b9a17 -r 768a8069bb8f test-data/.svn/prop-base/fillpeaks.RData.svn-base --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/prop-base/fillpeaks.RData.svn-base Fri Feb 19 11:32:06 2016 -0500 @@ -0,0 +1,5 @@ +K 13 +svn:mime-type +V 24 +application/octet-stream +END diff -r 6260844b9a17 -r 768a8069bb8f test-data/.svn/text-base/fillpeaks.RData.svn-base Binary file test-data/.svn/text-base/fillpeaks.RData.svn-base has changed diff -r 6260844b9a17 -r 768a8069bb8f test-data/.svn/text-base/report.html.svn-base --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/text-base/report.html.svn-base Fri Feb 19 11:32:06 2016 -0500 @@ -0,0 +1,74 @@ + + + + +[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 6260844b9a17 -r 768a8069bb8f xcms_report.tgz Binary file xcms_report.tgz has changed diff -r 6260844b9a17 -r 768a8069bb8f xcms_summary.r --- a/xcms_summary.r Fri Feb 19 11:00:57 2016 -0500 +++ b/xcms_summary.r Fri Feb 19 11:32:06 2016 -0500 @@ -89,13 +89,13 @@ md5sumHeaderHtml = "" md5sumHtml = "" md5sumLegend="" - } else if (!is.null(md5sumList$removalBadCharacters)) { + } else if (is.null(md5sumList$removalBadCharacters)) { md5sumHeaderHtml = paste("md5sum^*") md5sumHtml = paste("",md5sumList$origin,"") md5sumLegend = "
^*The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process." } else { md5sumHeaderHtml = paste("md5sum^*md5sum^** after bad characters removal") - md5sumHtml = paste("",md5sumList$origin,"",md5sumList$origin,"") + md5sumHtml = paste("",md5sumList$origin,"",md5sumList$removalBadCharacters,"") md5sumLegend = "
^*The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process.
^**Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.
" }

___ XCMS analysis summary using Workflow4Metabolomics ___

Samples used:

Function launched:

Information about the xcmsSet object:

Citations:

_ XCMS analysis summary using Workflow4Metabolomics _