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/tools/expression/norm.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<?xml version="1.0"?>
 2<tool id="normalise" name="Gene expression index" force_history_refresh="True">
 3<description>summarize and normalize expression data by RMA or MAS5.
 4</description>
 5<code file="norm_code.py"/>
 6<command interpreter="python">
 7norm.py '$opMode.i' '$opMode.title' '$logmeta' '$opMode.method'
 8</command>
 9 	
10<inputs>
11
12    <conditional name="opMode">
13
14       <param name="mode" type="select" label="Operation Type">
15            <option value="basic" selected="true">Basic</option>
16            <option value="advanced">Advanced</option>
17        </param>
18
19        <when value="basic">
20            <param name="title" label="Title to label the new output file" type="text" size="80"
21            value="Normalized" />
22            <param name="i" type="data" format="xys.zip,cel.zip"
23            label="File set chosen from your history" optional="false"
24            size="120" help="Choose a CEL/XYS file archive from your current history" />
25            <param name="method" type="hidden" value="rma"/>
26        </when>
27        <when value="advanced">
28            <param name="title" label="Title to label the new output file" type="text" size="80"
29            value="Normalised" />
30            <param name="i" type="data" format="xys.zip,cel.zip"
31            label="File set chosen from your history" optional="false"
32            size="120" help="Choose a CEL/XYS file archive from your current history" />
33            <param name="method" label="Normalisation method to apply" type="select" multiple="false">
34                <option value="rma" selected="True">rma</option>
35                <option value="justrma">justrma</option>
36                <option value="mas5">mas5</option>
37                <option value="gcrma">gcrma</option>
38            </param>
39        </when>
40
41    </conditional>
42
43   
44</inputs>
45
46<outputs>  
47    <data format='txt' name="logmeta"/>
48</outputs>
49
50<help>
51
52
53**Syntax**
54
55- **Title** is used to name the output files - so make it meaningful
56- **File set** is a .zip archive containing .CEL or .XYS files
57- **Normalisation method** is the algorithm to use to pre-process the input files
58
59-----
60
61This tool allows you to select from your galaxy history a raw data set of expression values (ZIP archive containing a set of Affymetrix .CEL or NimbleGen .XYS   files) and, calculate the expression index of this data set by performing the summarization and normalization of the data (four methods are available: RMA, justRMA, gcRMA and MAS5). Four gene expression files will be generated:
62
63 1. Probe Set ID annotated expression
64 2. Entrez annotated expression
65 3. RefSeq  annotated expression
66 4. An R object of type .eset that can be exported for further processing in R (if required)
67
68For Entrez and RefSeq annotation, custom CDF from BRAINARRAY (http://brainarray.mbni.med.umich.edu/) are used.
69
70Box plot and Histograms of both raw and normalized expression values will be also created as .pdf files.
71
72Note that this tool uses ideas documented at http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#biocon_affypack and uses standard R (www.r-project.org) and Bioconductor (htt://bioconductor.org) packages.
73
74Some base code for this tool was designed and written for the Rexpression BioC/Galaxy tools by ross lazarus (ross d0t lazarus at gmail d0t com) August 2008 Copyright Ross Lazarus 2008 Licensed under the LGPL as documented at http://www.gnu.org/licenses/lgpl.html
75
76</help>
77</tool>