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comparison AffyQCnormalization.xml @ 0:1024245abc70 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
author sblanck
date Thu, 22 Feb 2018 08:38:22 -0500
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1 <tool id="QCnormalization" name="QCnormalization" version="1.0.0">
2
3 <description>Quality control and normalization of affymetrix expression data</description>
4
5 <requirements>
6 <requirement type="package">bioconductor-biobase</requirement>
7 <requirement type="package">bioconductor-geoquery</requirement>
8 <requirement type="package">bioconductor-geometadb</requirement>
9 <requirement type="package">bioconductor-limma</requirement>
10 <requirement type="package">bioconductor-biobase</requirement>
11 <requirement type="package">bioconductor-affy</requirement>
12 <requirement type="package">bioconductor-affyPLM</requirement>
13 <requirement type="package">r-jsonlite</requirement>
14 <requirement type="package">r-dplyr</requirement>
15 <requirement type="package">r-optparse</requirement>
16 </requirements>
17
18 <stdio>
19 <exit_code range="1:" />
20 <regex match="Warning" source="both" level="warning"/>
21 </stdio>
22
23 <command>
24 <![CDATA[
25 Rscript
26 ${__tool_directory__}/AffyQCnormalization.R
27 --input "#for $input in $inputs# $input;$input.name, #end for#"
28 --normalization ${normalization}
29 --rdataoutput $result_export_eset
30 --htmloutput $result_html
31 --htmloutputpath $result_html.files_path
32 --htmltemplate ${__tool_directory__}/AffyQCnormalization_tpl.html
33 ]]>
34 </command>
35
36 <inputs>
37 <param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
38 <param name="normalization" type="select" label="Preprocessing/normalization">
39 <option value="rma">rma (backgroung correction + quantile normalization + log2)</option>
40 <option value="quantile">quantile normalization + log2</option>
41 <option value="background">background correction + log2</option>
42 <option value="log2">log2 only</option>
43 </param>
44 </inputs>
45
46 <outputs>
47 <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>
48 <data format="html" name="result_html" label="QC result"/>
49 </outputs>
50
51 <help>
52 <![CDATA[
53 **What it does**
54
55 The QCnormalization tool offers to ensure the quality of the data and to normalize them. Several normalization methods are available :
56
57 * rma normalization
58 * quantile normalization + log2
59 * background correction + log2
60 * log2 only
61
62 **Results**
63
64 - Several quality figures : microarray images, boxplots and MA plots
65 - Rdata object containing the normalized data for further analysis
66
67 ]]>
68 </help>
69
70 </tool>