Mercurial > repos > pieterlukasse > prims_metabolomics2

comparison xcms_get_mass_eic.xml @ 0:dffc38727496

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
initial commit
author pieter.lukasse@wur.nl
date Sat, 07 Feb 2015 22:02:00 +0100
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:dffc38727496
1 <tool id="xcms_get_mass_eic" name="XCMS Get EICs" version="0.0.4">
2 <description> Extracts EICs for a given list of masses</description>
3 <requirements>
4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
5 </requirements>
6 <command interpreter="Rscript">
7 xcms_get_mass_eic.r
8 $xsetData
9 $rtStart
10 $rtEnd
11 #if $massParameters.massParametersType == "window"
12 $massParameters.mzStart
13 $massParameters.mzEnd
14 -1
15 "."
16 #else
17 -1
18 -1
19 "$massParameters.mzList"
20 $massParameters.mzTolPpm
21 #end if
22 "$sampleNames"
23 $combineSamples
24 $rtPlotMode
25 $htmlReportFile
26 $htmlReportFile.files_path
27 $outLogFile
28 </command>
29 <inputs>
30
31 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
32
33
34 <param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" />
35 <param name="rtEnd" type="integer" value="" size="10" label="RT end" help="End of Retention Time region to plot" />
36
37 <conditional name="massParameters">
38 <param name="massParametersType" type="select" size="50" label="Give masses as" >
39 <option value="list" selected="true">m/z list</option>
40 <option value="window" >m/z window</option>
41 </param>
42 <when value="list">
43 <param name="mzList" type="text" area="true" size="7x70" label="m/z list"
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.">
45 <sanitizer>
46 <!-- this translates from line-separated to comma separated list, removes quotes -->
47 <valid/>
48 <mapping initial="none">
49 <add source="&#10;" target=","/>
50 <add source="&#13;" target=""/>
51 <add source="&quot;" target=""/>
52 </mapping>
53 </sanitizer>
54 </param>
55 <param name="mzTolPpm" type="integer" size="10" value="5" label="m/z tolerance (ppm)" />
56 </when>
57 <when value="window">
58 <param name="mzStart" type="float" value="" size="10" label="m/z start" help="Start of m/z window" />
59 <param name="mzEnd" type="float" value="" size="10" label="m/z end" help="End of m/z window" />
60 </when>
61 </conditional>
62
63
64 <param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names"
65 value="sampleName1,sampleName2,etc"
66 help="Comma or line-separated list of sample names. Here you can specify the subset of samples
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." >
68 <sanitizer>
69 <!-- this translates from line-separated to comma separated list, removes quotes -->
70 <valid/>
71 <mapping initial="none">
72 <add source="&#10;" target=","/>
73 <add source="&#13;" target=""/>
74 <add source="&quot;" target=""/>
75 </mapping>
76 </sanitizer>
77 </param>
78
79 <param name="combineSamples" type="select" size="50" label="Combine samples in EIC"
80 help="Combining samples means plot contains the combined EIC of a m/z in the different samples. When NOT combining, each plot
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
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
83 the different samples.">
84 <option value="No" selected="true">No</option>
85 <option value="Yes" >Yes</option>
86 </param>
87 <param name="rtPlotMode" type="select" size="50" label="RT plot mode"
88 help="Select whether EIC should be on original or raw Retention Time">
89 <option value="raw" selected="true">Raw</option>
90 <option value="corrected" >Corrected</option>
91 </param>
92 </inputs>
93 <outputs>
94 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
95 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/>
96 </outputs>
97 <tests>
98 <test>
99 </test>
100 </tests>
101 <help>
102
103 .. class:: infomark
104
105 This tool will plot EICs for a given list of masses (or a mass window) using XCMS's getEIC method.
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.
107
108 .. image:: $PATH_TO_IMAGES/massEIC.png
109
110
111 </help>
112 <citations>
113 <citation type="doi">10.1021/ac051437y</citation> <!-- example
114 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
115 -->
116 </citations>
117 </tool>