0
+ − 1 <tool id="xcms_get_mass_eic" name="XCMS Get EICs" version="0.0.4">
+ − 2 <description> Extracts EICs for a given list of masses</description>
+ − 3 <requirements>
+ − 4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+ − 5 </requirements>
+ − 6 <command interpreter="Rscript">
+ − 7 xcms_get_mass_eic.r
+ − 8 $xsetData
+ − 9 $rtStart
+ − 10 $rtEnd
+ − 11 #if $massParameters.massParametersType == "window"
+ − 12 $massParameters.mzStart
+ − 13 $massParameters.mzEnd
+ − 14 -1
+ − 15 "."
+ − 16 #else
+ − 17 -1
+ − 18 -1
+ − 19 "$massParameters.mzList"
+ − 20 $massParameters.mzTolPpm
+ − 21 #end if
+ − 22 "$sampleNames"
+ − 23 $combineSamples
+ − 24 $rtPlotMode
+ − 25 $htmlReportFile
+ − 26 $htmlReportFile.files_path
+ − 27 $outLogFile
+ − 28 </command>
+ − 29 <inputs>
+ − 30
+ − 31 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
+ − 32
+ − 33
+ − 34 <param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" />
+ − 35 <param name="rtEnd" type="integer" value="" size="10" label="RT end" help="End of Retention Time region to plot" />
+ − 36
+ − 37 <conditional name="massParameters">
+ − 38 <param name="massParametersType" type="select" size="50" label="Give masses as" >
+ − 39 <option value="list" selected="true">m/z list</option>
+ − 40 <option value="window" >m/z window</option>
+ − 41 </param>
+ − 42 <when value="list">
+ − 43 <param name="mzList" type="text" area="true" size="7x70" label="m/z list"
+ − 44 help="Comma or line-separated list of m/z values for which to plot an EIC. One EIC will be plotted for each m/z given here.">
+ − 45 <sanitizer>
+ − 46 <!-- this translates from line-separated to comma separated list, removes quotes -->
+ − 47 <valid/>
+ − 48 <mapping initial="none">
+ − 49 <add source=" " target=","/>
+ − 50 <add source=" " target=""/>
+ − 51 <add source=""" target=""/>
+ − 52 </mapping>
+ − 53 </sanitizer>
+ − 54 </param>
+ − 55 <param name="mzTolPpm" type="integer" size="10" value="5" label="m/z tolerance (ppm)" />
+ − 56 </when>
+ − 57 <when value="window">
+ − 58 <param name="mzStart" type="float" value="" size="10" label="m/z start" help="Start of m/z window" />
+ − 59 <param name="mzEnd" type="float" value="" size="10" label="m/z end" help="End of m/z window" />
+ − 60 </when>
+ − 61 </conditional>
+ − 62
+ − 63
+ − 64 <param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names"
+ − 65 value="sampleName1,sampleName2,etc"
+ − 66 help="Comma or line-separated list of sample names. Here you can specify the subset of samples
+ − 67 to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." >
+ − 68 <sanitizer>
+ − 69 <!-- this translates from line-separated to comma separated list, removes quotes -->
+ − 70 <valid/>
+ − 71 <mapping initial="none">
+ − 72 <add source=" " target=","/>
+ − 73 <add source=" " target=""/>
+ − 74 <add source=""" target=""/>
+ − 75 </mapping>
+ − 76 </sanitizer>
+ − 77 </param>
+ − 78
+ − 79 <param name="combineSamples" type="select" size="50" label="Combine samples in EIC"
+ − 80 help="Combining samples means plot contains the combined EIC of a m/z in the different samples. When NOT combining, each plot
+ − 81 only contains the EIC of the m/z in the respectively given sample (the sample name from the sample list in the same position as the
+ − 82 m/z in the m/z list.). Tip: use Yes for visualizing EIC of grouped masses (MsClust or CAMERA groups), use No for visualizing EICs of the same mass in
+ − 83 the different samples.">
+ − 84 <option value="No" selected="true">No</option>
+ − 85 <option value="Yes" >Yes</option>
+ − 86 </param>
+ − 87 <param name="rtPlotMode" type="select" size="50" label="RT plot mode"
+ − 88 help="Select whether EIC should be on original or raw Retention Time">
+ − 89 <option value="raw" selected="true">Raw</option>
+ − 90 <option value="corrected" >Corrected</option>
+ − 91 </param>
+ − 92 </inputs>
+ − 93 <outputs>
+ − 94 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
+ − 95 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/>
+ − 96 </outputs>
+ − 97 <tests>
+ − 98 <test>
+ − 99 </test>
+ − 100 </tests>
+ − 101 <help>
+ − 102
+ − 103 .. class:: infomark
+ − 104
+ − 105 This tool will plot EICs for a given list of masses (or a mass window) using XCMS's getEIC method.
+ − 106 It produces a HTML report showing the EIC plots, one for each given mass. The figure below shows an example of such an EIC plot.
+ − 107
+ − 108 .. image:: $PATH_TO_IMAGES/massEIC.png
+ − 109
+ − 110
+ − 111 </help>
+ − 112 <citations>
+ − 113 <citation type="doi">10.1021/ac051437y</citation> <!-- example
+ − 114 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+ − 115 -->
+ − 116 </citations>
+ − 117 </tool>
