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author pieter.lukasse@wur.nl
date Fri, 06 Feb 2015 15:49:26 +0100
parents 35f506f30ae4
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1 <tool id="xcms_get_alignment_eic" name="XCMS Get Alignment EICs" version="0.0.4">
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2 <description> Extracts alignment EICs from feature alignment data</description>
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3 <requirements>
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4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
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5 </requirements>
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6 <command interpreter="Rscript">
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7 xcms_get_alignment_eic.r
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8 $xsetData
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9 $rtStart
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10 $rtEnd
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11 $minNrSamples
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12 "$sampleNames"
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13 $htmlReportFile
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14 $htmlReportFile.files_path
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15 $outLogFile
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16 </command>
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17 <inputs>
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18
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19 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
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20
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21
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22 <param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" />
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23 <param name="rtEnd" type="integer" value="" size="10" label="RT end" help="End of Retention Time region to plot" />
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24
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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
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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." />
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27
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28 <param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names"
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29 value="sampleName1,sampleName2,etc"
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30 help="Comma or line-separated list of sample names. Optional field where you can specify the subset of samples
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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." >
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32 <sanitizer>
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33 <!-- this translates from line-separated to comma separated list, removes quotes -->
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34 <valid/>
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35 <mapping initial="none">
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36 <add source="&#10;" target=","/>
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37 <add source="&#13;" target=""/>
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38 <add source="&quot;" target=""/>
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39 </mapping>
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40 </sanitizer>
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41 </param>
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42
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43
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44 </inputs>
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45 <outputs>
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46 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
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47 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/>
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48 </outputs>
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49 <tests>
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50 <test>
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51 </test>
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52 </tests>
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53 <help>
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54
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55 .. class:: infomark
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56
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57 This tool finds the alignments in the specified RT window and extracts alignment EICs from feature alignment data using XCMS's getEIC method.
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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
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59 two classes, with extra alignment information beneath it.
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60
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61 .. image:: $PATH_TO_IMAGES/diffreport.png
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62
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63 Alignment id: 1709. m/z list of peaks in alignment:
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64 614.002922098482,613.998019830021,614.000382307519,613.998229980469,613.998229980469
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66
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67 </help>
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68 <citations>
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69 <citation type="doi">10.1021/ac051437y</citation> <!-- example
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70 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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71 -->
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72 </citations>
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73 </tool>