comparison minfi_ppfun.xml @ 8:432fd69157fa draft

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author kpbioteam
date Fri, 22 Feb 2019 08:12:22 -0500
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7:f47e5cca1696 8:432fd69157fa
1 <tool id="minfi_ppfun" name="Minfi Preprocess Funnorm" version="@MINFI_VERSION@">
2 <description>implements the functional normalization algorithm</description><macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="requirements">
6 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
7 </expand>
8 <command detect_errors="exit_code">
9 <![CDATA[
10 Rscript '$minfi_pp_script'
11 ]]>
12 </command>
13 <configfiles>
14 <configfile name="minfi_pp_script"><![CDATA[
15 require("minfi", quietly = TRUE)
16 RGSet <- get(load('$rgset'))
17
18 GRSet <- preprocessFunnorm(RGSet)
19
20 save(GRSet,file = '$grset')
21 ]]>
22 </configfile>
23 </configfiles>
24
25 <inputs>
26 <param type="data" name="rgset" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
27 </inputs>
28 <outputs>
29 <data name="grset" format="rdata" label="GenomicRatioSet"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="rgset" value="RGChannelSet.rdata"/>
34 <output name="grset" file="FunGenomicRatioSet.rdata"/>
35 </test>
36 </tests>
37 <help><![CDATA[
38 This tool uses the internal control probes present on the array to infer between-array technical variation. It is particularly useful for studies comparing conditions with known large-scale differences, such as cancer/normal studies, or between-tissue studies. It has been shown that for such studies, functional normalization outperforms other existing approaches (Jean-Philippe Fortin et al. 2014).
39 ]]></help>
40 <expand macro="citations" />
41 </tool>