41
+ − 1 <tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate" version="0.0.3">
+ − 2 <description> Runs metaMS process for LC/MS feature grouping and annotation</description>
+ − 3 <requirements>
+ − 4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+ − 5 </requirements>
+ − 6 <command interpreter="Rscript">
+ − 7 metaMS_cmd_interface.r
+ − 8 $constructed_db
+ − 9 $data_files
+ − 10 $customMetaMSsettings
+ − 11 $outputFile
+ − 12 $outputLog
+ − 13 $xsetOut
+ − 14 $htmlReportFile
+ − 15 $htmlReportFile.files_path
+ − 16 </command>
+ − 17 <inputs>
+ − 18 <param name="constructed_db" type="select" label="Constructed DB" help="Reference annotation database generated from matching measurements of a mixture of chemical standards
+ − 19 against a manually validated reference table which contains the key analytical information for each standard."
+ − 20 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/>
+ − 21
+ − 22 <param name="data_files" type="data" format="prims.fileset.zip" label="Data files (.zip file with CDFs)" help=".zip file containing the CDF files of the new measurements"/>
+ − 23
+ − 24
+ − 25
+ − 26 <param name="protocolName" type="text" size="30" label="protocolName" value="Synapt.QTOF.RP" help="protocolName"/>
+ − 27
+ − 28 <param name="method" type="select" size="30" label="PEAK PICKING method =====================================================">
+ − 29 <option value="matchedFilter" selected="true">matchedFilter</option>
+ − 30 </param>
+ − 31 <param name="step" type="float" size="10" value="0.05" label="step" help="step"/>
+ − 32 <param name="fwhm" type="integer" size="10" value="20" label="fwhm" help="fwhm" />
+ − 33 <param name="snthresh" type="integer" size="10" value="4" label="snthresh" help="snthresh" />
+ − 34 <param name="max" type="integer" size="10" value="50" label="max" help="max" />
+ − 35
+ − 36 <param name="min_class_fraction" type="float" size="10" value="0.3" label="ALIGNMENT min.class.fraction =====================================================" help="min.class.fraction"/>
+ − 37 <param name="min_class_size" type="integer" size="10" value="3" label="min.class.size" help="min.class.size" />
+ − 38 <param name="mzwid" type="float" size="10" value="0.1" label="mzwid" help="mzwid"/>
+ − 39 <param name="bws" type="text" size="10" value="30,10" label="bws" help="bws"/>
+ − 40 <param name="missingratio" type="float" size="10" value="0.2" label="missingratio" help="missingratio"/>
+ − 41 <param name="extraratio" type="float" size="10" value="0.1" label="extraratio" help="extraratio"/>
+ − 42 <param name="retcormethod" type="select" size="30" label="retcormethod" help="retcormethod">
+ − 43 <option value="linear" selected="true">linear</option>
+ − 44 </param>
+ − 45 <param name="retcorfamily" type="select" size="30" label="retcorfamily" help="retcorfamily">
+ − 46 <option value="symmetric" selected="true">symmetric</option>
+ − 47 </param>
+ − 48 <param name="fillPeaks" type="select" size="30" label="fillPeaks" help="fillPeaks">
+ − 49 <option value="TRUE" selected="true">Yes</option>
+ − 50 <option value="FALSE">No</option>
+ − 51 </param>
+ − 52 <param name="perfwhm" type="float" size="10" value="0.6" label="CAMERA perfwhm =====================================================" help="perfwhm"/>
+ − 53 <param name="cor_eic_th" type="float" size="10" value="0.7" label="cor_eic_th" help="cor_eic_th" />
+ − 54 <param name="ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
+ − 55 <param name="rtdiff" type="float" size="10" value="1.5" label="MATCH2DB rtdiff =====================================================" help="rtdiff"/>
+ − 56 <param name="rtval" type="float" size="10" value="0.1" label="rtval" help="rtval" />
+ − 57 <param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="mzdiff" />
+ − 58 <param name="match2DB_ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
+ − 59 <param name="minfeat" type="integer" size="10" value="2" label="minfeat" help="minfeat" />
+ − 60
+ − 61 </inputs>
+ − 62 <configfiles>
+ − 63
+ − 64 <configfile name="customMetaMSsettings">## start comment
+ − 65 ## metaMS process settings
+ − 66 customMetaMSsettings <- metaMSsettings(protocolName = "${protocolName}",
+ − 67 chrom = "LC",
+ − 68 PeakPicking = list(
+ − 69 method = "${method}",
+ − 70 step = ${step},
+ − 71 fwhm = ${fwhm},
+ − 72 snthresh = ${snthresh},
+ − 73 max = ${max}),
+ − 74 Alignment = list(
+ − 75 min.class.fraction = ${min_class_fraction},
+ − 76 min.class.size = ${min_class_size},
+ − 77 mzwid = ${mzwid},
+ − 78 bws = c(${bws}),
+ − 79 missingratio = ${missingratio},
+ − 80 extraratio = ${extraratio},
+ − 81 retcormethod = "${retcormethod}",
+ − 82 retcorfamily = "${retcorfamily}",
+ − 83 fillPeaks = ${fillPeaks}),
+ − 84 CAMERA = list(
+ − 85 perfwhm = ${perfwhm},
+ − 86 cor_eic_th = ${cor_eic_th},
+ − 87 ppm= ${ppm}))
+ − 88 metaSetting(customMetaMSsettings, "match2DB") <- list(
+ − 89 rtdiff = ${rtdiff},
+ − 90 rtval = ${rtval},
+ − 91 mzdiff = ${mzdiff},
+ − 92 ppm = ${match2DB_ppm},
+ − 93 minfeat = ${minfeat})</configfile>
+ − 94
+ − 95 </configfiles>
+ − 96
+ − 97 <outputs>
+ − 98 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - metaMS annotated file (TSV)"/>
+ − 99 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG"/>
+ − 100 <data name="xsetOut" format="rdata" label="${tool.name} on ${on_string} - metaMS xcmsSet (RDATA)"/>
+ − 101 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/>
+ − 102 </outputs>
+ − 103 <tests>
+ − 104 <test>
+ − 105 </test>
+ − 106 </tests>
+ − 107 <code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
+ − 108 <help>
+ − 109
+ − 110 .. class:: infomark
+ − 111
+ − 112 Runs metaMS process for LC/MS feature grouping and annotation. Parts of the metaMS process also make use of the XCMS and CAMERA tools and algorithms.
+ − 113 The figure below shows the main parts of the metaMS process.
+ − 114
+ − 115 .. image:: $PATH_TO_IMAGES/metaMS.png
+ − 116
+ − 117
+ − 118 **References**
+ − 119
+ − 120 If you use this Galaxy tool in work leading to a scientific publication please
+ − 121 cite the following papers:
+ − 122
+ − 123 Wehrens, R.; Weingart, G.; Mattivi, F. (2014).
+ − 124 metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics.
+ − 125 Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116.
+ − 126 doi: 10.1016/j.jchromb.2014.02.051
+ − 127 handle: http://hdl.handle.net/10449/24012
+ − 128
+ − 129
+ − 130 </help>
+ − 131 <citations>
+ − 132 <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example
+ − 133 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+ − 134 -->
+ − 135 </citations>
+ − 136 </tool>
