<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>