# HG changeset patch # User lecorguille # Date 1438959748 14400 # Node ID f3f97841564fb2e89716d0fe79c9c0c0794bfb11 Uploaded diff -r 000000000000 -r f3f97841564f abims_xcms_group.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_group.xml Fri Aug 07 11:02:28 2015 -0400 @@ -0,0 +1,266 @@ + + + Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. + + + R + Rscript + xcms + xcms_w4m_script + + + + + + + + xcms.r + xfunction group image $image method $methods.method sleep 0.001 + #if $methods.method == "density": + ## minsamp $methods.minsamp + minfrac $methods.minfrac + bw $methods.bw + mzwid $methods.mzwid + #if $methods.density_options.option == "show": + max $methods.density_options.max + #end if + #elif $methods.method == "mzClust": + mzppm $methods.mzppm + mzabs $methods.mzabs + minfrac $methods.minfrac + ## minsamp $methods.minsamp + #else: + mzVsRTbalance $methods.mzVsRTbalance + mzCheck $methods.mzCheck + rtCheck $methods.rtCheck + kNN $methods.kNN + #end if + && ( + mv group.RData $xsetRData; + mv Rplots.pdf $rplotsPdf + ); + 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 + +**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.Group +========== + +----------- +Description +----------- + +After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class. + + + +----------------- +Workflow position +----------------- + +**Upstream tools** + +========================= ================= =================== ========== +Name output file format parameter +========================= ================= =================== ========== +xcms.xcmsSet xset.RData rdata.xcms.raw RData file +------------------------- ----------------- ------------------- ---------- +xcms.retcor xset.RData rdata.xcms.retcor RData file +========================= ================= =================== ========== + + +**Downstream tools** + ++---------------------------+--------------------------------------+ +| Name | Output file | Format | ++===========================+=================+====================+ +|xcms.retcor | xset.RData | rdata.xcms.group | ++---------------------------+--------------------------------------+ +|xcms.fillPeaks | xset.RData | rdata.xcms.group | ++---------------------------+--------------------------------------+ + +The output file is an xcmsSet.RData file. You can continue your analysis using it in **xcms.retcor** tool as an next step and then **xcms.fillPeaks**. + +**General schema of the metabolomic workflow** + +.. image:: xcms_group_workflow.png + + +----------- +Input files +----------- + ++---------------------------+-----------------------+ +| Parameter : num + label | Format | ++===========================+=======================+ +| 1 : RData file | rdata.xcms.group | ++---------------------------+-----------------------+ + + +---------- +Parameters +---------- + +Method to use for grouping +-------------------------- + +**mzClust** + + | Runs high resolution alignment on single spectra samples stored in the RData file generated by the **xcmsSet tool**. + +**density** + + | Groups peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. + +**nearest** + + | Groups peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine. + + +------------ +Output files +------------ + +xset.group.Rplots.pdf + +xset.group.RData: rdata.xcms.group format + + | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks). + + +------ + +.. class:: infomark + +The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool. + + +--------------------------------------------------- + + +--------------- +Working example +--------------- + +Input files +----------- + + | RData file -> **xset.RData** + +Parameters +---------- + + | Method -> **density** + | bw -> **5** + | minfrac -> **0.3** + | mzwid -> **0.01** + | Advanced options: **show** + | max -> **50** + + +Output files +------------ + + | **1) xset.RData: RData file** + + | **2) Example of an xset.group.Rplots pdf file** + +.. image:: xcms_group.png + :width: 700 + + + + + + + 10.1021/ac051437y + 10.1093/bioinformatics/btu813 + + + + diff -r 000000000000 -r f3f97841564f repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Aug 07 11:02:28 2015 -0400 @@ -0,0 +1,4 @@ + + + + diff -r 000000000000 -r f3f97841564f static/images/xcms_group.png Binary file static/images/xcms_group.png has changed diff -r 000000000000 -r f3f97841564f static/images/xcms_group_workflow.png Binary file static/images/xcms_group_workflow.png has changed diff -r 000000000000 -r f3f97841564f test-data/xset.RData Binary file test-data/xset.RData has changed diff -r 000000000000 -r f3f97841564f test-data/xset.group.RData Binary file test-data/xset.group.RData has changed diff -r 000000000000 -r f3f97841564f test-data/xset.group.Rplots.pdf Binary file test-data/xset.group.Rplots.pdf has changed diff -r 000000000000 -r f3f97841564f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Aug 07 11:02:28 2015 -0400 @@ -0,0 +1,12 @@ + + + + + + + + + + + +