Mercurial > repos > pieterlukasse > prims_metabolomics2

comparison metaMS/xcms_get_alignment_eic.xml @ 6:4393f982d18f

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
reorganized sources
author pieter.lukasse@wur.nl
date Thu, 19 Mar 2015 12:22:23 +0100
parents
children
comparison
equal deleted inserted replaced
5:41f122255d14 6:4393f982d18f
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 $outLogFile
16 </command>
17 <inputs>
18
19 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
20
21
22 <param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" />
23 <param name="rtEnd" type="integer" value="" size="10" label="RT end" help="End of Retention Time region to plot" />
24
25 <param name="minNrSamples" type="integer" size="10" value="10" label="Minimum number of samples in which aligned feature should be found" help="Can also read this as: Minimum
26 number of features in alignment. E.g. if set to 10, it means the alignment should consist of at least 10 peaks from 10 different samples aligned together." />
27
28 <param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names"
29 value="sampleName1,sampleName2,etc"
30 help="Comma or line-separated list of sample names. Optional field where you can specify the subset of samples
31 to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." >
32 <sanitizer>
33 <!-- this translates from line-separated to comma separated list, removes quotes -->
34 <valid/>
35 <mapping initial="none">
36 <add source="&#10;" target=","/>
37 <add source="&#13;" target=""/>
38 <add source="&quot;" target=""/>
39 </mapping>
40 </sanitizer>
41 </param>
42
43
44 </inputs>
45 <outputs>
46 <data name="outLogFile" format="txt" label="${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>