Mercurial > repos > pieterlukasse > prims_metabolomics2
view metams_lcms_annotate.xml @ 0:dffc38727496
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author | pieter.lukasse@wur.nl |
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date | Sat, 07 Feb 2015 22:02:00 +0100 |
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<tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate" version="0.0.4"> <description> Runs metaMS process for LC/MS feature annotation</description> <requirements> <requirement type="package" version="3.1.1">R_bioc_metams</requirement> </requirements> <command interpreter="Rscript"> metaMS_cmd_annotate.r $constructed_db $xsetData $customMetaMSsettings $outputFile #if $mzTol.mzTolType == "fixed" 0 #else "$mzTol.mass_error_function" #end if $htmlReportFile $htmlReportFile.files_path $outputLog </command> <inputs> <param name="constructed_db" type="select" label="Constructed DB" help="Reference annotation database generated from matching measurements of a mixture of chemical standards against a manually validated reference table which contains the key analytical information for each standard." dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/> <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="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)"/> <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> <configfile name="customMetaMSsettings">## start comment ## metaMS process settings customMetaMSsettings <- metaMSsettings(protocolName = "${protocolName}", chrom = "LC") metaSetting(customMetaMSsettings, "match2DB") <- list( rtdiff = ${rtdiff}, rtval = ${rtval}, #if $mzTol.mzTolType == "fixed" mzdiff = ${mzTol.mzdiff}, #else ppm = ${mzTol.ppm}, #end if minfeat = ${minfeat})</configfile> </configfiles> <outputs> <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - metaMS annotated file (TSV)"/> <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG" hidden="True"/> <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/> </outputs> <tests> <test> </test> </tests> <code file="match_library.py" /> <!-- file containing get_directory_files function used above--> <help> .. class:: infomark 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_annotate.png .. class:: infomark The implemented annotation strategy can be broken down in the following steps: 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. 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> <citations> <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set --> </citations> </tool>