# HG changeset patch # User lecorguille # Date 1438959456 14400 # Node ID 19c1d2598eb5a667f5c221a9264c5143782c7fe9 planemo upload diff -r 000000000000 -r 19c1d2598eb5 Makefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Fri Aug 07 10:57:36 2015 -0400 @@ -0,0 +1,23 @@ +# USAGE: make [install|clean] + +# -------- VARIABLE -------- + +OBJ=xcms_retcor.tgz +DEP=abims_xcms_retcor.xml tool_dependencies.xml repository_dependencies.xml static test-data + + +# ------------------------ + +all: $(OBJ) + +$(OBJ): $(DEP) + tar --exclude=".svn" -zchf $@ $^ + +# ------------------------ + +install: $(OBJ) + mv *.tgz ~ + +clean: + rm *.tgz + diff -r 000000000000 -r 19c1d2598eb5 abims_xcms_retcor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_retcor.xml Fri Aug 07 10:57:36 2015 -0400 @@ -0,0 +1,276 @@ + + + Retention Time Correction using retcor function from xcms R package + + + R + Rscript + xcms + xcms_w4m_script + + + + + + + + xcms.r + image $image xfunction retcor 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 + && ( mv retcor.RData $xsetRData; + mv TICs_corrected.pdf $ticsCorPdf ; + mv BPCs_corrected.pdf $bpcsCorPdf ; + mv Rplots.pdf $rplotsPdf 2> /dev/null); + cat xset.log; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (methods['method'] == 'peakgroups') + (options['option'] == 'show') + (family == 'symmetric') + (plottype != 'none') + + + + + + + + + + + + + + + + + + + + + + + + + + +.. 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 + + + + + 10.1021/ac051437y + 10.1093/bioinformatics/btu813 + + + diff -r 000000000000 -r 19c1d2598eb5 planemo.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo.sh Fri Aug 07 10:57:36 2015 -0400 @@ -0,0 +1,1 @@ +planemo shed_init -f --name=xcms_retcor --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples" --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\nRetention Time Correction using retcor function from xcms R package\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics" diff -r 000000000000 -r 19c1d2598eb5 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Aug 07 10:57:36 2015 -0400 @@ -0,0 +1,5 @@ + + + + + diff -r 000000000000 -r 19c1d2598eb5 static/images/xcms_retcor.png Binary file static/images/xcms_retcor.png has changed diff -r 000000000000 -r 19c1d2598eb5 static/images/xcms_retcor_workflow.png Binary file static/images/xcms_retcor_workflow.png has changed diff -r 000000000000 -r 19c1d2598eb5 test-data/xset.group.RData Binary file test-data/xset.group.RData has changed diff -r 000000000000 -r 19c1d2598eb5 test-data/xset.group.retcor.BPCs_corrected.pdf Binary file test-data/xset.group.retcor.BPCs_corrected.pdf has changed diff -r 000000000000 -r 19c1d2598eb5 test-data/xset.group.retcor.RData Binary file test-data/xset.group.retcor.RData has changed diff -r 000000000000 -r 19c1d2598eb5 test-data/xset.group.retcor.Rplots.pdf Binary file test-data/xset.group.retcor.Rplots.pdf has changed diff -r 000000000000 -r 19c1d2598eb5 test-data/xset.group.retcor.TICs_corrected.pdf Binary file test-data/xset.group.retcor.TICs_corrected.pdf has changed diff -r 000000000000 -r 19c1d2598eb5 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Aug 07 10:57:36 2015 -0400 @@ -0,0 +1,12 @@ + + + + + + + + + + + +