Mercurial > repos > lecorguille > xcms_summary

changeset 1:768a8069bb8f draft

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Uploaded
author lecorguille
date Fri, 19 Feb 2016 11:32:06 -0500
parents 6260844b9a17
children 0b87dcf08f72
files Makefile README.rst planemo.sh test-data/.svn/entries test-data/.svn/prop-base/fillpeaks.RData.svn-base test-data/.svn/text-base/fillpeaks.RData.svn-base test-data/.svn/text-base/report.html.svn-base xcms_report.tgz xcms_summary.r
diffstat 9 files changed, 177 insertions(+), 34 deletions(-) [+]
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--- 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
-
--- 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
-
--- 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"
--- /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
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+dir
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+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
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+2016-02-19T15:58:48.218379Z
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+fillpeaks.RData
+file
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+2016-02-19T15:55:14.364130Z
+ad9e3cfef6c684bc4203efb101445274
+2016-02-19T15:58:48.218379Z
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+2016-02-19T15:55:14.364130Z
+f1b08eb3da7992bd6627032dcc82362a
+2016-02-19T15:58:48.218379Z
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--- /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
Binary file test-data/.svn/text-base/fillpeaks.RData.svn-base has changed
--- /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 @@
+<!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>
Binary file xcms_report.tgz has changed
--- 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$removalBadCharacters)) {
             md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>")
             md5sumHtml = paste("<td>",md5sumList$origin,"</td>")
             md5sumLegend = "<br/><sup>*</sup>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("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
-            md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$origin,"</td>")
+            md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>")
             md5sumLegend = "<br/><sup>*</sup>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.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"
         }