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minfi_maptogenome.xml |
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| diff -r 3511473319c2 -r 7d6e9bd197b8 minfi_maptogenome.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_maptogenome.xml Fri Feb 22 08:13:15 2019 -0500 |
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| @@ -0,0 +1,43 @@ +<tool id="minfi_maptogenome" name="Minfi map to genome" version="@MINFI_VERSION@"> + <description>mapping Ilumina methylation array data to the genome</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 '$minfi_mtg_script' + ]]> + </command> + <configfiles> + <configfile name="minfi_mtg_script"><![CDATA[ +require("minfi", quietly = TRUE) +require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE) + +RSet <- get(load('$rset')) + +GRSet <- mapToGenome(RSet) + +save(GRSet,file = '$grset') + ]]> + </configfile> + </configfiles> + <inputs> + <param type="data" name="rset" format="rdata" label="Methylation Data to Map" help="This class holds preprocessed data for Illumina methylation microarrays." /> + </inputs> + <outputs> + <data name="grset" format="rdata" from_work_dir="GRSet.rdata" label= "Data Mapped To The Genome" /> + </outputs> + <tests> + <test> + <param name="rset" value="RatioSet.rdata"/> + <output name="grset" file="GRSet.rdata"/> + </test> + </tests> + <help><![CDATA[ + This tool is mapping Ilumina methylation array data to the genome using 450k annotation package. Depending on the genome, not all methylation loci may have a genomic position. The output is an a GenomicRatioSet object. + ]]></help> + <expand macro="citations" /> +</tool> |