Mercurial > repos > kpbioteam > ewastools
comparison minfi_ppfun.xml @ 8:432fd69157fa draft
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| author | kpbioteam |
|---|---|
| date | Fri, 22 Feb 2019 08:12:22 -0500 |
| parents | |
| children | 9c6fbb7d5a2a |
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| 7:f47e5cca1696 | 8:432fd69157fa |
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| 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> |