6
+ − 1 <tool id="xcms_get_alignment_eic" name="XCMS Get Alignment EICs" version="0.0.4">
+ − 2 <description> Extracts alignment EICs from feature alignment data</description>
+ − 3 <requirements>
+ − 4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+ − 5 </requirements>
+ − 6 <command interpreter="Rscript">
+ − 7 xcms_get_alignment_eic.r
+ − 8 $xsetData
+ − 9 $rtStart
+ − 10 $rtEnd
+ − 11 $minNrSamples
+ − 12 "$sampleNames"
+ − 13 $htmlReportFile
+ − 14 $htmlReportFile.files_path
+ − 15 $outLogFile
+ − 16 </command>
+ − 17 <inputs>
+ − 18
+ − 19 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
+ − 20
+ − 21
+ − 22 <param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" />
+ − 23 <param name="rtEnd" type="integer" value="" size="10" label="RT end" help="End of Retention Time region to plot" />
+ − 24
+ − 25 <param name="minNrSamples" type="integer" size="10" value="10" label="Minimum number of samples in which aligned feature should be found" help="Can also read this as: Minimum
+ − 26 number of features in alignment. E.g. if set to 10, it means the alignment should consist of at least 10 peaks from 10 different samples aligned together." />
+ − 27
+ − 28 <param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names"
+ − 29 value="sampleName1,sampleName2,etc"
+ − 30 help="Comma or line-separated list of sample names. Optional field where you can specify the subset of samples
+ − 31 to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." >
+ − 32 <sanitizer>
+ − 33 <!-- this translates from line-separated to comma separated list, removes quotes -->
+ − 34 <valid/>
+ − 35 <mapping initial="none">
+ − 36 <add source=" " target=","/>
+ − 37 <add source=" " target=""/>
+ − 38 <add source=""" target=""/>
+ − 39 </mapping>
+ − 40 </sanitizer>
+ − 41 </param>
+ − 42
+ − 43
+ − 44 </inputs>
+ − 45 <outputs>
+ − 46 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
+ − 47 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/>
+ − 48 </outputs>
+ − 49 <tests>
+ − 50 <test>
+ − 51 </test>
+ − 52 </tests>
+ − 53 <help>
+ − 54
+ − 55 .. class:: infomark
+ − 56
+ − 57 This tool finds the alignments in the specified RT window and extracts alignment EICs from feature alignment data using XCMS's getEIC method.
+ − 58 It produces a HTML report showing the EIC plots and the mass list of each alignment. The figure below shows an example of such an EIC plot, showing also the difference between
+ − 59 two classes, with extra alignment information beneath it.
+ − 60
+ − 61 .. image:: $PATH_TO_IMAGES/diffreport.png
+ − 62
+ − 63 Alignment id: 1709. m/z list of peaks in alignment:
+ − 64 614.002922098482,613.998019830021,614.000382307519,613.998229980469,613.998229980469
+ − 65
+ − 66
+ − 67 </help>
+ − 68 <citations>
+ − 69 <citation type="doi">10.1021/ac051437y</citation> <!-- example
+ − 70 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+ − 71 -->
+ − 72 </citations>
+ − 73 </tool>
