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minfi_getbeta.xml |
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| diff -r db44217b3c5d -r 8833eedd24fb minfi_getbeta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_getbeta.xml Fri Feb 22 08:14:44 2019 -0500 |
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| @@ -0,0 +1,41 @@ +<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> |