| Previous changeset 51:52cf1f7f11c5 (2019-02-22) Next changeset 53:5cab527307f9 (2019-02-22) |
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minfi_mset.xml |
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| diff -r 52cf1f7f11c5 -r dc2c96a82f56 minfi_mset.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_mset.xml Fri Feb 22 11:12:33 2019 -0500 |
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| @@ -0,0 +1,41 @@ +<tool id="minfi_mset" name="Minfi mset" version="@MINFI_VERSION@"> + <description>Create objects contains CpGs signals</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> + <![CDATA[ + Rscript '$minfi_mset_script' + ]]> + </command> + <configfiles> + <configfile name="minfi_mset_script"><![CDATA[ +require("minfi", quietly = TRUE) + +RGSet <- get(load('$RGChannelSet')) + +MSet <- preprocessRaw(RGSet) + +save(MSet,file = '$MethylSet') + + ]]> + </configfile> + </configfiles> + <inputs> + <param type="data" name="RGChannelSet" 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="MethylSet" format="rdata" label="MethylSet" /> + </outputs> + <tests> + <test> + <param name="RGChannelSet" value="RGChannelSet.rdata"/> + <output name="MethylSet" file="MethylSet.rdata"/> + </test> + </tests> + <help><![CDATA[ + This tool is transforming a class representing raw (unprocessed) data from a two color micro array - RGChannelSet into a class holding preprocessed data for Illumina methylation microarrays, mapped to genomic location - MethylSet. + ]]></help> + <expand macro="citations" /> +</tool> |