Mercurial > repos > pieterlukasse > prims_metabolomics
annotate xcms_get_mass_eic.xml @ 57:963684611ccb
fix for xcms support in msclust
author | pieter.lukasse@wur.nl |
---|---|
date | Fri, 12 Dec 2014 12:06:36 +0100 |
parents | f772a5caa86a |
children | 35f506f30ae4 |
rev | line source |
---|---|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
1 <tool id="xcms_get_mass_eic" name="XCMS Get EICs" version="0.0.4"> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
2 <description> Extracts EICs for a given list of masses</description> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
3 <requirements> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
5 </requirements> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
6 <command interpreter="Rscript"> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
7 xcms_get_mass_eic.r |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
8 $xsetData |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
9 $rtStart |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
10 $rtEnd |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
11 #if $massParameters.massParametersType == "window" |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
12 $massParameters.mzStart |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
13 $massParameters.mzEnd |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
14 -1 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
15 "." |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
16 #else |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
17 -1 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
18 -1 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
19 $massParameters.mzList |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
20 $massParameters.mzTolPpm |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
21 #end if |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
22 "$sampleNames" |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
23 $combineSamples |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
24 $rtPlotMode |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
25 $htmlReportFile |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
26 $htmlReportFile.files_path |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
27 $outLogFile |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
28 </command> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
29 <inputs> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
30 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
31 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
32 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
33 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
34 <param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" /> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
35 <param name="rtEnd" type="integer" value="" size="10" label="RT end" help="End of Retention Time region to plot" /> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
36 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
37 <conditional name="massParameters"> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
38 <param name="massParametersType" type="select" size="50" label="Give masses as" > |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
39 <option value="list" selected="true">m/z list</option> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
40 <option value="window" >m/z window</option> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
41 </param> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
42 <when value="list"> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
43 <param name="mzList" type="text" area="true" size="7x70" label="m/z list" |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
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."> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
45 <sanitizer> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
46 <!-- this translates from line-separated to comma separated list --> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
47 <valid/> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
48 <mapping initial="none"> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
49 <add source=" " target=","/> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
50 <add source=" " target=""/> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
51 </mapping> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
52 </sanitizer> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
53 </param> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
54 <param name="mzTolPpm" type="integer" size="10" value="5" label="m/z tolerance (ppm)" /> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
55 </when> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
56 <when value="window"> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
57 <param name="mzStart" type="float" value="" size="10" label="m/z start" help="Start of m/z window" /> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
58 <param name="mzEnd" type="float" value="" size="10" label="m/z end" help="End of m/z window" /> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
59 </when> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
60 </conditional> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
61 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
62 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
63 <param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names" |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
64 value="sampleName1,sampleName2,etc" |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
65 help="Comma or line-separated list of sample names. Here you can specify the subset of samples |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
66 to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." > |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
67 <sanitizer> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
68 <valid/> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
69 <mapping initial="none"> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
70 <add source=" " target=","/> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
71 <add source=" " target=""/> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
72 </mapping> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
73 </sanitizer> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
74 </param> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
75 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
76 <param name="combineSamples" type="select" size="50" label="Combine samples in EIC" |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
77 help="Combining samples means plot contains the combined EIC of a m/z in the different samples. When NOT combining, each plot |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
78 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 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
79 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 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
80 the different samples."> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
81 <option value="No" selected="true">No</option> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
82 <option value="Yes" >Yes</option> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
83 </param> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
84 <param name="rtPlotMode" type="select" size="50" label="RT plot mode" |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
85 help="Select whether EIC should be on original or raw Retention Time"> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
86 <option value="raw" selected="true">Raw</option> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
87 <option value="corrected" >Corrected</option> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
88 </param> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
89 </inputs> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
90 <outputs> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
91 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
92 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
93 </outputs> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
94 <tests> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
95 <test> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
96 </test> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
97 </tests> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
98 <help> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
99 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
100 .. class:: infomark |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
101 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
102 This tool will plot EICs for a given list of masses (or a mass window) using XCMS's getEIC method. |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
103 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. |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
104 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
105 .. image:: $PATH_TO_IMAGES/massEIC.png |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
106 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
107 |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
108 </help> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
109 <citations> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
110 <citation type="doi">10.1021/ac051437y</citation> <!-- example |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
111 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
112 --> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
113 </citations> |
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff
changeset
|
114 </tool> |