| Previous changeset 52:5b1adc49700d (2014-12-11) Next changeset 54:10f3cb998c4e (2014-12-11) |
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Commit message:
small fixes |
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modified:
metaMS_cmd_annotate.r metams_lcms_annotate.xml metams_lcms_pick_and_group.xml |
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added:
static/images/metaMS_annotate.png static/images/metaMS_pick_align_camera.png |
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| diff -r 5b1adc49700d -r 70574a6381ea metaMS_cmd_annotate.r --- a/metaMS_cmd_annotate.r Thu Dec 11 10:26:17 2014 +0100 +++ b/metaMS_cmd_annotate.r Thu Dec 11 14:09:27 2014 +0100 |
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| @@ -10,13 +10,16 @@ ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt" args.outAnnotationTable <- args[4] +args.mass_error_function <- args[5] +if (args.mass_error_function == "0") + args.mass_error_function <- NULL ## report files -args.htmlReportFile <- args[5] -args.htmlReportFile.files_path <- args[6] +args.htmlReportFile <- args[6] +args.htmlReportFile.files_path <- args[7] -if (length(args) == 7) +if (length(args) == 8) { - args.outLogFile <- args[7] + args.outLogFile <- args[8] # suppress messages: # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888 msg <- file(args.outLogFile, open="wt") @@ -43,7 +46,7 @@ # Just to highlight: if you want to use more than one # trigger runLC: - LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE) + LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, errf=args.mass_error_function, nSlaves=20, returnXset = TRUE) # write out runLC annotation results: write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE) @@ -52,7 +55,7 @@ cat("\nConstructed DB info===============:\n") str(tempEnv[[testDB[1]]]$Info) cat("\nConstructed DB table===============:\n") - if (length(args) == 7) + if (length(args) == 8) { write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE) write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE) |
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| diff -r 5b1adc49700d -r 70574a6381ea metams_lcms_annotate.xml --- a/metams_lcms_annotate.xml Thu Dec 11 10:26:17 2014 +0100 +++ b/metams_lcms_annotate.xml Thu Dec 11 14:09:27 2014 +0100 |
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| @@ -9,6 +9,11 @@ $xsetData $customMetaMSsettings $outputFile + #if $mzTol.mzTolType == "fixed" + 0 + #else + "$mzTol.mass_error_function" + #end if $htmlReportFile $htmlReportFile.files_path $outputLog @@ -20,13 +25,31 @@ <param name="xsetData" type="data" format="rdata" label="xcmsSet data file (xset RDATA)" help="E.g. output data file resulting from METAMS 'feature picking, aligning and grouping' run"/> - <param name="protocolName" type="text" size="30" label="protocolName" value="Synapt.QTOF.RP" help="protocolName"/> + <param name="protocolName" type="text" size="30" label="protocolName" value="e.g. Synapt.QTOF.RP" + help="Choose a name to give for the specific settings in the parameters below"/> + + <param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="(Annotation) Allowed rt difference (in minutes)"/> - <param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="rtdiff"/> - <param name="rtval" type="float" size="10" value="0.1" label="rtval" help="rtval" /> - <param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="mzdiff" /> - <param name="match2DB_ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" /> - <param name="minfeat" type="integer" size="10" value="2" label="minfeat" help="minfeat" /> + <conditional name="mzTol"> + <param name="mzTolType" type="select" size="30" label="(Annotation) m/z tolerance type"> + <option value="fixed" selected="true">Fixed tolerance</option> + <option value="adaptive" >Adaptive tolerance</option> + </param> + <when value="fixed"> + <param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="(Annotation) Fixed mass tolerance" /> + </when> + <when value="adaptive"> + <param name="ppm" type="float" size="10" value="5.0" label="ppm" help="(Annotation) Tolerance in ppm" /> + <param name="mass_error_function" type="text" area="true" size="3x70" label="(Annotation) Mass error function"/> + </when> + </conditional> + + <param name="rtval" type="float" size="10" value="0.1" label="(max)rtval" help="(Validation) Group items are clustered once more with hierarchical clustering ('complete' method) + based on their rt distances. Here one can specify the rt threshold for removing the items that have too diverging rt (the ones with rt difference + larger than rtval). " /> + <param name="minfeat" type="integer" size="10" value="2" label="minfeat" + help="(Validation) Threshold for the minimum number of features a + cluster/group should have (after rtval filtering above). Other clusters/groups are filtered out." /> </inputs> <configfiles> @@ -38,8 +61,11 @@ metaSetting(customMetaMSsettings, "match2DB") <- list( rtdiff = ${rtdiff}, rtval = ${rtval}, - mzdiff = ${mzdiff}, - ppm = ${match2DB_ppm}, + #if $mzTol.mzTolType == "fixed" + mzdiff = ${mzTol.mzdiff}, + #else + ppm = ${mzTol.ppm}, + #end if minfeat = ${minfeat})</configfile> </configfiles> @@ -58,27 +84,32 @@ .. class:: infomark -Runs metaMS process for LC/MS feature annotation. -The figure below shows the main parts of the metaMS process. -This tool related to the last step of this process. +Runs metaMS process for LC/MS feature annotation based on matching to an existing 'standards' DB. +The figure below shows the main parts of this metaMS process. -.. image:: $PATH_TO_IMAGES/metaMS.png +.. image:: $PATH_TO_IMAGES/metaMS_annotate.png -From CAMERA documentation: +.. class:: infomark -.. image:: $PATH_TO_IMAGES/CAMERA_results.png - -**References** +The implemented annotation strategy can be broken down in the following steps: -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: +1. *Feature wise Annotation:* Each feature detected by runLC is matched against the database. If +the mass error function is provided, the appropriate m/z tolerance is calculated, otherwise a fixed +tolerance is used (mzdiff). The retention time tolerance is fixed and should be selected on the +bases of the characteristics of each chromatographic method (rtdiff). Multiple annotations - i.e. +features which are associated to more than one compound - are possible. This outcome does not +indicate a problem per se, but is an inherent drawback of co-elution. -Wehrens, R.; Weingart, G.; Mattivi, F. (2014). -metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics. -Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116. -doi: 10.1016/j.jchromb.2014.02.051 -handle: http://hdl.handle.net/10449/24012 +2. *Annotation Validation:* The annotated features are organized in 'pseudospectra' collecting all +the experimental features which are assigned to a specific compound. A specific annotation is +confirmed only if more than minfeat features which differ in retention time less than rtval are +present in a pseudospectrum. As a general rule rtval should be narrower than rtdiff. The +latter, indeed, accounts for shifts in retention time between the injection of the standards and the +metabolomics experiment under investigation. This time can be rather long, considering that the +standards are not commonly re-analyzed each time. On the other hand, rtval represents the shift +between the ions of the same compound within the same batch of injections and therefore it has +only to account for the smaller shifts occurring during peak picking and alignment. </help> |
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| diff -r 5b1adc49700d -r 70574a6381ea metams_lcms_pick_and_group.xml --- a/metams_lcms_pick_and_group.xml Thu Dec 11 10:26:17 2014 +0100 +++ b/metams_lcms_pick_and_group.xml Thu Dec 11 14:09:27 2014 +0100 |
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| @@ -269,10 +269,14 @@ Runs metaMS process for LC/MS feature feature picking, aligning and grouping. This part of the metaMS process makes use of the XCMS and CAMERA tools and algorithms. CAMERA is used for automatic deconvolution/annotation of LC/ESI-MS data. -The figure below shows the main parts of the metaMS process. +The figure below shows the main parts of the metaMS process wrapped by this tool. + +.. image:: $PATH_TO_IMAGES/metaMS_pick_align_camera.png -.. image:: $PATH_TO_IMAGES/metaMS.png +From CAMERA documentation: + +.. image:: $PATH_TO_IMAGES/CAMERA_results.png **References** |
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| diff -r 5b1adc49700d -r 70574a6381ea static/images/metaMS_annotate.png |
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| Binary file static/images/metaMS_annotate.png has changed |
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| diff -r 5b1adc49700d -r 70574a6381ea static/images/metaMS_pick_align_camera.png |
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| Binary file static/images/metaMS_pick_align_camera.png has changed |
