Mercurial > repos > lecorguille > xcms_report
changeset 8:2cb130282060 draft
Uploaded
| author | lecorguille |
|---|---|
| date | Wed, 23 Dec 2015 11:07:20 -0500 |
| parents | e18100ba8c10 |
| children | 17d585d877ee |
| files | abims_xcms_report.xml abims_xcms_retcor.xml planemo.sh repository_dependencies.xml static/images/xcms_retcor.png static/images/xcms_retcor_workflow.png test-data/.svn/entries test-data/.svn/props/fillpeaks.RData.svn-work test-data/fillpeaks.RData test-data/log.txt test-data/report.html test-data/sacuri.zip test-data/xset.group.RData test-data/xset.group.retcor.BPCs_corrected.pdf test-data/xset.group.retcor.RData test-data/xset.group.retcor.Rplots.pdf test-data/xset.group.retcor.TICs_corrected.pdf tool_dependencies.xml xcms_report.r |
| diffstat | 19 files changed, 412 insertions(+), 277 deletions(-) [+] |
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--- a/abims_xcms_report.xml Wed Dec 23 09:30:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ -<tool id="abims_xcms_report" name="xcms.report" version="0.1.0"> - - <description>Create a report of XCMS analysis</description> - - <requirements> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="binary">Rscript</requirement> - <requirement type="package" version="1.44.0">xcms</requirement> - </requirements> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - - <command interpreter="Rscript"><![CDATA[ - xcms_report.r - - image $image - htmlOutput $htmlOutput - user_email $__user_email__ - - ]]></command> - - <inputs> - - <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" /> - - </inputs> - - <outputs> - <data name="htmlOutput" format="html" label="xcms report html" /> - </outputs> - - <tests> - <test> - <param name="image" value="fillpeaks.RData" /> - <output name="htmlOutput" file="report.html" /> - </test> - </tests> - - <help><![CDATA[ - -.. class:: infomark - -**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff part of Workflow4Metabolomics.org [W4M] - - | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. - ---------------------------------------------------- - -============ -Xcms.report -============ - ------------ -Description ------------ - -This tool provide a HTML report which summarizes your analysis using the [W4M] XCMS and CAMERA tools - - - ]]></help> - - - <citations> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> - -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_retcor.xml Wed Dec 23 11:07:20 2015 -0500 @@ -0,0 +1,301 @@ +<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.4"> + + <description>Retention Time Correction using retcor function from xcms R package </description> + + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="binary">Rscript</requirement> + <requirement type="package" version="1.44.0">xcms</requirement> + <requirement type="package" version="2.1">xcms_w4m_script</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command><![CDATA[ + xcms.r + image $image + xfunction retcor + + xsetRdataOutput $xsetRData + ticspdf $ticsCorPdf + bicspdf $bpcsCorPdf + rplotspdf $rplotsPdf + + method $methods.method + #if $methods.method == "obiwarp": + profStep $methods.profStep + #else + smooth $methods.smooth + extra $methods.extra + missing $methods.missing + #if $methods.options.option == "show": + span $methods.options.span + family $methods.options.family + plottype $methods.options.plottype + #end if + #end if + #if $zip_file: + zipfile $zip_file + #end if + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" + + ]]></command> + + <inputs> + <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> + <conditional name="methods"> + <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > + <option value="obiwarp" >obiwarp</option> + <option value="peakgroups" selected="peakgroups">peakgroups</option> + </param> + <when value="obiwarp"> + <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" /> + </when> + <when value="peakgroups"> + <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" > + <option value="loess">loess</option> + <option value="linear">linear</option> + </param> + <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" /> + <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" /> + <conditional name="options"> + <param name="option" type="select" label="Advanced options"> + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/> + + <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> + <option value="gaussian" selected="true">gaussian</option> + <option value="symmetric">symmetric</option> + </param> + + <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> + <option value="none" selected="true">none</option> + <option value="deviation">deviation</option> + <option value="mdevden">mdevden</option> + </param> + </when> + <when value="hide"> + </when> + </conditional> + </when> + </conditional> + <!-- To pass planemo test --> + <param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" /> + </inputs> + + <outputs> + <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" /> + <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf"> + <filter>(methods['method'] == 'peakgroups')</filter> + <filter>(options['option'] == 'show')</filter> + <filter>(family == 'symmetric')</filter> + <filter>(plottype != 'none')</filter> + </data> + <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" /> + <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" /> + <data name="log" format="txt" label="xset.log.txt" hidden="true" /> + </outputs> + + <tests> + <test> + <param name="image" value="xset.group.RData"/> + <param name="methods.method" value="peakgroups"/> + <param name="methods.smooth" value="loess"/> + <param name="methods.extra" value="1"/> + <param name="methods.missing" value="1"/> + <param name="methods.options.option" value="show"/> + <param name="methods.options.span" value="0.2"/> + <param name="methods.options.family" value="gaussian"/> + <param name="methods.options.plottype" value="deviation"/> + <param name="zip_file" value="sacuri.zip"/> + <!--<output name="xsetRData" file="xset.group.retcor.RData" />--> + <!--<output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />--> + <!--<output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />--> + <!--<output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />--> + <output name="log"> + <assert_contents> + <has_text text="object with 9 samples" /> + <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" /> + <has_text text="Mass range: 50.0019-999.9863 m/z" /> + <has_text text="Peaks: 135846 (about 15094 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: bio, blank" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ + + +.. class:: infomark + +**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu + +.. class:: infomark + +**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M] + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + + + +--------------------------------------------------- + +=========== +Xcms.retcor +=========== + +----------- +Description +----------- + +After matching peaks into groups, xcms can use those groups to identify and correct +correlated drifts in retention time from run to run. The aligned peaks can then be +used for a second pass of peak grouping which will be more accurate than the first. +The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful +for identifying retention time drifts. Some groups may be missing peaks from a large +fraction of samples and thus provide an incomplete picture of the drift at that time point. +Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping. + +.. class:: warningmark + +**After an retcor step, it is mandatory to do a group step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is +discarded)** + + + +----------------- +Workflow position +----------------- + + +**Upstream tools** + +========================= ================= ======= ========== +Name output file format parameter +========================= ================= ======= ========== +xcms.group xset.group.RData RData RData file +========================= ================= ======= ========== + + +**Downstream tools** + ++---------------------------+------------------+--------+ +| Name | Output file | Format | ++===========================+==================+========+ +|xcms.group | xset.retcor.RData| RData | ++---------------------------+------------------+--------+ + +The output file **xset.retcor.RData** is an RData file. You can continue your analysis using it in **xcms.group** tool as an next step. + + +**General schema of the metabolomic workflow** + +.. image:: xcms_retcor_workflow.png + + +----------- +Input files +----------- + ++---------------------------+----------------------+ +| Parameter : num + label | Format | ++===========================+======================+ +| 1 : RData file | rdata.xcms.group | ++---------------------------+----------------------+ + + +---------- +Parameters +---------- + +Method +------ + +**peakgroups** + + | xcms ignores those groups by only considering well-behaved peak groups which are missing at most one sample and have at most one extra peak. (Those values can be changed with the **missing** and **extra** arguments.) + | For each of those well-behaved groups, the algorithm calculates a median retention time and, for every sample, a deviation from that median. Within a sample, the observed deviation generally changes over time in a nonlinear fashion. Those changes are approximated using a local polynomial regression technique implemented in the **loess** function. By default, the curve fitting is done using least-squares on all data points. + | However, it is possible to enable outlier detection and removal by setting the **family** argument to **symmetric**. + +**obiwarp** + + | Calculate retention time deviations for each sample using the obiwarp code at "http://obi-warp.sourceforge.net/". This function is able to align multiple samples by a center-star strategy. Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. OBI-Warp harnesses the non-linear, comprehensive alignment power of DTW and builds on the discrete, non-bijective output of DTW to give natural interpolants that can be used across multiple datasets. + | For the original publication see :**Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpo-lated Warping John T. Prince and, Edward M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152.** + + +------------ +Output files +------------ + +xset.group.retcor.TICs_corrected.pdf + + | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step. + +xset.group.retcor.BPCs_corrected.pdf + + | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step + +xset.group.retcor.RData: rdata.xcms.retcor format + + | Rdata file that will be necessary in the **xcms.group** step of the workflow. + + +------ + +.. class:: infomark + +The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool. + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +----------- + + | RData file -> **xset.group.RData** + +Parameters +---------- + + | Method: -> **peakgroups** + | smooth: -> **loess** + | extra: -> **1** + | missing -> **1** + | Advanced options: -> **show** + | span -> **0.2** + | family -> **gaussian** + | plottype -> **deviation** + + +Output files +------------ + + | **1) xset.group.retcor.RData: RData file** + + | **2) Example of an xset.group.retcor.TICs_corrected pdf file** + +.. image:: xcms_retcor.png + + ]]></help> + + <citations> + <citation type="doi">10.1021/ac051437y</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + +</tool>
--- a/planemo.sh Wed Dec 23 09:30:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -planemo shed_init -f --name=xcms_report --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - HTML Report 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 report of XCMS analysis" --category="Metabolomics"
--- a/repository_dependencies.xml Wed Dec 23 09:30:57 2015 -0500 +++ b/repository_dependencies.xml Wed Dec 23 11:07:20 2015 -0500 @@ -1,4 +1,5 @@ <?xml version="1.0"?> <repositories> - <repository name="rdata_xcms_datatypes" owner="lecorguille" /> + <repository changeset_revision="9ed593071db2" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="bff835d58914" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/entries Wed Dec 23 11:07:20 2015 -0500 @@ -0,0 +1,49 @@ +10 + +dir +0 +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_report/test-data +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo +add + + + + + + + + + + + + + + + + + + + +87d02074-be8c-4456-a071-04b64888326c + +fillpeaks.RData +file + + + +add + + + + + +has-props +has-prop-mods + +report.html +file + + + +add +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/props/fillpeaks.RData.svn-work Wed Dec 23 11:07:20 2015 -0500 @@ -0,0 +1,5 @@ +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log.txt Wed Dec 23 11:07:20 2015 -0500 @@ -0,0 +1,52 @@ + PACKAGE INFO +parallel 3.1.2 +BiocGenerics 0.14.0 +Biobase 2.28.0 +Rcpp 0.12.0 +mzR 2.2.2 +xcms 1.44.0 +snow 0.3.13 +batch 1.1.4 + + + ARGUMENTS INFO +image test-data/xset.group.RData +xfunction retcor +xsetRdataOutput test-data/xset.group.retcor.RData +ticspdf xset.group.retcor.TICs_corrected.pdf +bicspdf xset.group.retcor.BPCs_corrected.pdf +rplotspdf xset.group.retcor.Rplots.pdf +method obiwarp +profStep 1 +zipfile test-data/sacuri.zip + + + INFILE PROCESSING INFO + + + ARGUMENTS PROCESSING INFO + + + MAIN PROCESSING INFO +center sample: HU_neg_060 +Processing: HU_neg_028 HU_neg_051 HU_neg_017 HU_neg_034 Blanc09 Blanc06 Blanc12 Blanc04 +null device + 1 + + + XSET OBJECT INFO +An "xcmsSet" object with 9 samples + +Time range: 0.7-1139.9 seconds (0-19 minutes) +Mass range: 50.0019-999.9863 m/z +Peaks: 135846 (about 15094 per sample) +Peak Groups: 0 +Sample classes: bio, blank + +Profile settings: method = bin + step = 0.01 + +Memory usage: 13.8 MB + + + DONE
--- a/test-data/report.html Wed Dec 23 09:30:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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 report</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 report 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>
--- a/tool_dependencies.xml Wed Dec 23 09:30:57 2015 -0500 +++ b/tool_dependencies.xml Wed Dec 23 11:07:20 2015 -0500 @@ -6,4 +6,7 @@ <package name="xcms" version="1.44.0"> <repository changeset_revision="8ea252413ed6" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> + <package name="xcms_w4m_script" version="2.1"> + <repository changeset_revision="af163ca0ac33" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> </tool_dependency>
--- a/xcms_report.r Wed Dec 23 09:30:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,132 +0,0 @@ -#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file -# version="0.1.0" -#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM - - - -# ----- ARGUMENTS BLACKLIST ----- -#xcms.r -argBlacklist=c("zipfile","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf") -#CAMERA.r -argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path") - -# ----- PACKAGE ----- - -pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch") -for(pkg in pkgs) { - suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) -} - - -# ----- FUNCTION ----- -writehtml = function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") } - - -# ----- ARGUMENTS ----- - -listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects - - -# ----- ARGUMENTS PROCESSING ----- - -#image is an .RData file necessary to use xset variable given by previous tools -load(listArguments[["image"]]); - -htmlOutput = "report.html" -if (!is.null(listArguments[["htmlOutput"]])){ - htmlOutput = listArguments[["htmlOutput"]]; -} - -user_email = NULL -if (!is.null(listArguments[["user_email"]])){ - user_email = listArguments[["user_email"]]; -} - - -# ----- MAIN PROCESSING INFO ----- -writehtml("<!DOCTYPE html>") -writehtml("<HTML lang='en'>") - -writehtml("<HEAD>") - writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />") - - writehtml("<title>[W4M] XCMS analysis report</title>") - - writehtml("<style>") - writehtml("table { min-width: 500px; border:1px solid #D6B161; border-collapse:collapse;}") - writehtml("th { background: #898989; text-align:left;}") - writehtml("tr { border: 1px solid #000000 }") - writehtml("h2 { color: #FFA212; }") - writehtml("ul li { margin-bottom:10px; }") - writehtml("</style>") -writehtml("</HEAD>") - -writehtml("<BODY>") - writehtml("<h1>___ XCMS analysis report using Workflow4Metabolomics ___</h1>") - # to pass the planemo shed_test - if (user_email != "test@bx.psu.edu") { - if (!is.null(user_email)) writehtml("By: ",user_email," - ") - writehtml("Date: ",format(Sys.time(), "%y%m%d-%H:%M:%S")) - } - - - writehtml("<h2>Samples used:</h2>") - writehtml("<table") - writehtml("<tr><th>sample</th><th>filename</th></tr>") - writehtml(paste("<tr><td>",sampnames(xset),"</td><td>",xset@filepaths,"</td></tr>")) - writehtml("</table>") - - writehtml("<h2>Function launched:</h2>") - writehtml("<table>") - writehtml("<tr><th>timestamp<br />(ymd-h:m:s)</th><th>function</th><th>argument</th><th>value</th></tr>") - for(tool in names(listOFlistArguments)) { - listOFlistArgumentsDisplay=listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)] - - timestamp = strsplit(tool,"_")[[1]][1] - xcmsFunction = strsplit(tool,"_")[[1]][2] - writehtml("<tr><td rowspan='",length(listOFlistArgumentsDisplay),"'>",timestamp,"</td><td rowspan='",length(listOFlistArgumentsDisplay),"'>",xcmsFunction,"</td>") - line_begin="" - for (arg in names(listOFlistArgumentsDisplay)) { - writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>") - line_begin="<tr>" - } - } - writehtml("</table>") - - writehtml("<h2>Information about the xcmsSet object:</h2>") - - log_file=file(htmlOutput, open = "at") - writehtml("<pre>") - sink(log_file) - sink(log_file, type = "output") - xset - sink() - writehtml("</pre>") - - writehtml("<h2>Citations:</h2>") - writehtml("<ul>") - writehtml("<li>To cite the <b>XCMS</b> package in publications use:") - writehtml("<ul>") - writehtml("<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>") - writehtml("<li>","Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)","</li>") - writehtml("<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>") - writehtml("</ul>") - writehtml("</li>") - - writehtml("<li>To cite the <b>CAMERA</b> package in publications use:") - writehtml("<ul>") - writehtml("<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>") - writehtml("</ul>") - writehtml("</li>") - - writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:") - writehtml("<ul>") - writehtml("<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>") - writehtml("</ul>") - writehtml("</li>") - writehtml("</ul>") - -writehtml("</BODY>") - -writehtml("</HTML>") -