|
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> |
