<tool id="minfi_getM" name="Minfi Get M" version="@MINFI_VERSION@">
    <description>returns the Fisher information corresponding to a model and a design</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
     Rscript '$minfi_m_script'
    ]]>
    </command>
    <configfiles>
    <configfile name="minfi_m_script"><![CDATA[
require("minfi", quietly = TRUE)
MSet <- get(load('$mset'))

m <- getM(MSet)

write.table(m, '$matrix')
 ]]> 
    </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="txt" label="M Value Matrix"/>
    </outputs>
    <tests>
        <test>
            <param name="mset" value="MethylSet.rdata"/>
            <output name="matrix" file="M_Value_Matrix.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool output M value the logit representation of methylation level ratio based on intensities between methylated and unmethylated alleles in each probed CpG site.
    ]]></help>
    <expand macro="citations" />
</tool>