annotate xcms_get_alignment_eic.xml @ 49:f772a5caa86a

Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.
author pieter.lukasse@wur.nl
date Wed, 10 Dec 2014 22:03:27 +0100
parents
children 35f506f30ae4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
49
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
1 <tool id="xcms_get_alignment_eic" name="XCMS Get Alignment EICs" version="0.0.4">
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
2 <description> Extracts alignment EICs from feature alignment data</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_alignment_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 $minNrSamples
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
12 "$sampleNames"
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
13 $htmlReportFile
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
14 $htmlReportFile.files_path
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
15 $outLogFile
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
16 </command>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
17 <inputs>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
18
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
19 <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
20
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
21
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
22 <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
23 <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
24
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
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
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
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." />
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
27
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
28 <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
29 value="sampleName1,sampleName2,etc"
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
30 help="Comma or line-separated list of sample names. Optional field where you can specify the subset of samples
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
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." >
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
32 <sanitizer>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
33 <!-- this translates from line-separated to comma separated list -->
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
34 <valid/>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
35 <mapping initial="none">
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
36 <add source="&#10;" target=","/>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
37 <add source="&#13;" target=""/>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
38 </mapping>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
39 </sanitizer>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
40 </param>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
41
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
42
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
43 </inputs>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
44 <outputs>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
45 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
46 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
47 </outputs>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
48 <tests>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
49 <test>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
50 </test>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
51 </tests>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
52 <help>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
53
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
54 .. class:: infomark
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
55
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
56 This tool finds the alignments in the specified RT window and extracts alignment EICs from feature alignment data using XCMS's getEIC method.
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
57 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
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
58 two classes, with extra alignment information beneath it.
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
59
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
60 .. image:: $PATH_TO_IMAGES/diffreport.png
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 Alignment id: 1709. m/z list of peaks in alignment:
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
63 614.002922098482,613.998019830021,614.000382307519,613.998229980469,613.998229980469
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
64
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
65
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
66 </help>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
67 <citations>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
68 <citation type="doi">10.1021/ac051437y</citation> <!-- example
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
69 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
70 -->
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
71 </citations>
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
72 </tool>