Mercurial > repos > kpbioteam > ewastools
view minfi_getbeta.xml @ 73:4caf1f2a4a65 draft
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author | kpbioteam |
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date | Fri, 10 May 2019 06:44:02 -0400 |
parents | 8833eedd24fb |
children | 9c6fbb7d5a2a |
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<tool id="minfi_getbeta" name="Minfi Get Beta" version="@MINFI_VERSION@"> <description>obtain Beta value matrix</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ Rscript '$minfi_beta_script' ]]> </command> <configfiles> <configfile name="minfi_beta_script"><![CDATA[ require("minfi", quietly = TRUE) MSet <- get(load('$mset')) beta <- getBeta(MSet) write.table(beta, file = '$matrix', quote = FALSE, sep = "\t") ]]> </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="matrix" format="bedgraph" label="Beta Values Matrix"/> </outputs> <tests> <test> <param name="mset" value="MethylSet.rdata"/> <output name="matrix" file="Beta_Values_Matrix.bedgraph"/> </test> </tests> <help><![CDATA[ This tools outputs an interval file of methylation indices (beta values), which are continuous values between 0 and 1 representing the ratio/fraction of the intensity of the methylated-probe signal to the total signal intensity for each probed CpG site. ]]></help> <expand macro="citations" /> </tool>