|
8
|
1 <tool id="xcms_differential_analysis" name="XCMS Differential Analsysis" version="0.0.1">
|
|
|
2 <description> Runs xcms diffreport function for differential Analsysis</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="Rscript">
|
|
|
7 xcms_differential_analysis.r
|
|
|
8 $xsetData
|
|
|
9 $class1
|
|
|
10 $class2
|
|
|
11 $topcount
|
|
|
12 $outTable
|
|
|
13 $outLogFile
|
|
|
14 $htmlReportFile
|
|
|
15 $htmlReportFile.files_path
|
|
|
16 </command>
|
|
|
17 <inputs>
|
|
|
18
|
|
|
19 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
|
|
|
20
|
|
|
21
|
|
|
22 <param name="class1" type="text" size="30" label="Class1 name" value="" help="Name of first class for the comparison"/>
|
|
|
23 <param name="class2" type="text" size="30" label="Class2 name" value="" help="Name of second class for the comparison"/>
|
|
|
24
|
|
|
25 <param name="topcount" type="integer" size="10" value="10" label="Number of items to return" help="Top X differential items. E.g. if 10, it will return top 10 differential items." />
|
|
|
26
|
|
|
27 </inputs>
|
|
|
28 <outputs>
|
|
|
29 <data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/>
|
|
|
30 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - differential log (LOG)"/>
|
|
|
31 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/>
|
|
|
32 </outputs>
|
|
|
33 <tests>
|
|
|
34 <test>
|
|
|
35 </test>
|
|
|
36 </tests>
|
|
|
37 <help>
|
|
|
38
|
|
|
39 .. class:: infomark
|
|
|
40
|
|
|
41 Runs xcms diffreport for showing the most significant differences between two sets/classes of samples. This tool also creates extracted ion chromatograms (EICs) for
|
|
|
42 the most significant differences. The figure below shows an example of such an EIC.
|
|
|
43
|
|
|
44 .. image:: $PATH_TO_IMAGES/diffreport.png
|
|
|
45
|
|
|
46
|
|
|
47
|
|
|
48
|
|
|
49 </help>
|
|
|
50 <citations>
|
|
|
51 <citation type="doi">10.1021/ac051437y</citation> <!-- example
|
|
|
52 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
|
|
|
53 -->
|
|
|
54 </citations>
|
|
|
55 </tool> |
