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minfi_ppfun.xml |
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| diff -r f47e5cca1696 -r 432fd69157fa minfi_ppfun.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_ppfun.xml Fri Feb 22 08:12:22 2019 -0500 |
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| @@ -0,0 +1,41 @@ +<tool id="minfi_ppfun" name="Minfi Preprocess Funnorm" version="@MINFI_VERSION@"> + <description>implements the functional normalization algorithm</description><macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> + </expand> + <command detect_errors="exit_code"> + <![CDATA[ + Rscript '$minfi_pp_script' + ]]> + </command> + <configfiles> + <configfile name="minfi_pp_script"><![CDATA[ +require("minfi", quietly = TRUE) +RGSet <- get(load('$rgset')) + +GRSet <- preprocessFunnorm(RGSet) + +save(GRSet,file = '$grset') + ]]> + </configfile> + </configfiles> + +<inputs> + <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." /> + </inputs> + <outputs> + <data name="grset" format="rdata" label="GenomicRatioSet"/> + </outputs> + <tests> + <test> + <param name="rgset" value="RGChannelSet.rdata"/> + <output name="grset" file="FunGenomicRatioSet.rdata"/> + </test> + </tests> + <help><![CDATA[ + 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). + ]]></help> + <expand macro="citations" /> +</tool> |