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