| Previous changeset 3:5549088d4c65 (2019-02-22) Next changeset 5:ab6e72fdf350 (2019-02-22) |
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added:
minfi_rset.xml |
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| diff -r 5549088d4c65 -r 8a3d5d8a433f minfi_rset.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_rset.xml Fri Feb 22 08:10:56 2019 -0500 |
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| @@ -0,0 +1,40 @@ +<tool id="minfi_rset" name="Minfi rset" version="@MINFI_VERSION@"> + <description>store Beta values and/or M values</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> + <![CDATA[ + Rscript '$read_rset_script' + ]]> + </command> + <configfiles> + <configfile name="read_rset_script"> + <![CDATA[ +require("minfi", quietly = TRUE) +MSet <- get(load('$mset')) + +RSet <- ratioConvert(MSet, what = "both", keepCN = TRUE) + +save(RSet,file = '$rset') + ]]> </configfile> + </configfiles> + <inputs> + <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic +location."/> + </inputs> + <outputs> + <data name="rset" format="rdata" label="RatioSet"/> + </outputs> + <tests> + <test> + <param name="mset" value="MethylSet.rdata"/> + <output name="rset" file="RatioSet.rdata"/> + </test> + </tests> + <help><![CDATA[ + RSet class holds preprocessed data for Illumina methylation microarrays. It contains respectively the Beta value matrix, M value matrix and the Copy Number matrix. + ]]></help> + <expand macro="citations" /> +</tool> |