# HG changeset patch # User lecorguille # Date 1438940150 14400 # Node ID 30b01bcefda477ec2229491371c38c4ba30a9fef planemo upload diff -r 000000000000 -r 30b01bcefda4 Makefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Fri Aug 07 05:35:50 2015 -0400 @@ -0,0 +1,23 @@ +# USAGE: make [install|clean] + +# -------- VARIABLE -------- + +OBJ=xcms_fillpeaks.tgz +DEP=abims_xcms_fillPeaks.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 30b01bcefda4 abims_xcms_fillPeaks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_fillPeaks.xml Fri Aug 07 05:35:50 2015 -0400 @@ -0,0 +1,183 @@ + + + Integrate the signal in the region of that peak group not represented and create a new peak + + + R + Rscript + xcms + xcms_w4m_script + + + + + + + + xcms.r xfunction fillPeaks image $image method $method && mv fillPeaks.RData $xsetRData; cat xset.log + + + + + + + + + + + + + + + + + + + + + + + + + +.. 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.fillPeaks +============== + +----------- +Description +----------- + +For each sample, identify peak groups where that sample is not +represented. For each of those peak groups, integrate the signal +in the region of that peak group and create a new peak. + +According to the type of raw-data there are 2 +different methods available. for filling gcms/lcms data the method +"chrom" integrates raw-data in the chromatographic domain, whereas +"MSW" is used for peaklists without retention-time information +like those from direct-infusion spectra. + + + +----------------- +Workflow position +----------------- + + +**Upstream tools** + +========================= ================= ================== ========== +Name output file format parameter +========================= ================= ================== ========== +xcms.group xset.group.RData rdata.xcms.group RData file +========================= ================= ================== ========== + + +**Downstream tools** + ++---------------------------+------------------+-----------------------+ +| Name | Output file | Format | ++===========================+==================+=======================+ +|xcms.diffreport | xset.retcor.RData| rdata.xcms.fillpeaks | ++---------------------------+------------------+-----------------------+ +|xcms.annotateDiffreport | xset.retcor.RData| rdata.xcms.fillpeaks | ++---------------------------+------------------+-----------------------+ + +The output file **xset.fillpeaks** is an RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool as an next step of the workflow. + + +**General schema of the metabolomic workflow** + +.. image:: xcms_fillpeaks_workflow.png + + + +----------- +Input files +----------- + ++---------------------------+-----------------------+ +| Parameter : num + label | Format | ++===========================+=======================+ +| 1 : RData file | rdata.xcms.group | ++---------------------------+-----------------------+ + + +---------- +Parameters +---------- + + +Method +------ + +**chrom** + + | This method produces intensity values for those missing samples by integrating raw data in peak group region. In a given group, the start and ending retention time points for integration are defined by the median start and end points of the other detected peaks. The start and end m/z values are similarly determined. Intensities can be still be zero, which is a rather unusual intensity for a peak. This is the case if e.g. the raw data was threshholded, and the integration area contains no actual raw intensities, or if one sample is miscalibrated, such the raw data points are (just) outside the integration area. + | Importantly, if retention time correction data is available, the alignment information is used to more precisely integrate the propper region of the raw data. If the corrected retention time is beyond the end of the raw data, the value will be not-a-number (NaN). + +**MSW** + + | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra. + +------------ +Output files +------------ + +xset.fillPeaks.RData : rdata.xcms.fillpeaks format + + | Rdata file that will be used in the **xcms.diffreport** or **xcms.annotateDiffreport** step of the workflow. + +------ + +.. class:: infomark + +The output file is an group.RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool. + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +----------- + + | RData file -> **xset.retcor.RData** + +Parameters +---------- + + | method -> **chrom** + + +Output files +------------ + + | **xset.fillPeaks.RData: RData file** + + + + + + 10.1021/ac051437y + 10.1093/bioinformatics/btu813 + + + + diff -r 000000000000 -r 30b01bcefda4 planemo.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo.sh Fri Aug 07 05:35:50 2015 -0400 @@ -0,0 +1,1 @@ +planemo shed_init -f --name=xcms_fillpeaks --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Integrate areas of missing peaks" --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\nFor each sample, identify peak groups where that sample is not represented. For each of those peak groups, integrate the signal in the region of that peak group and create a new peak.\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 30b01bcefda4 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Aug 07 05:35:50 2015 -0400 @@ -0,0 +1,5 @@ + + + + + diff -r 000000000000 -r 30b01bcefda4 static/images/xcms_fillpeaks_workflow.png Binary file static/images/xcms_fillpeaks_workflow.png has changed diff -r 000000000000 -r 30b01bcefda4 test-data/xset.group.retcor.group.RData Binary file test-data/xset.group.retcor.group.RData has changed diff -r 000000000000 -r 30b01bcefda4 test-data/xset.group.retcor.group.fillPeaks.RData Binary file test-data/xset.group.retcor.group.fillPeaks.RData has changed diff -r 000000000000 -r 30b01bcefda4 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Aug 07 05:35:50 2015 -0400 @@ -0,0 +1,12 @@ + + + + + + + + + + + +