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minfi_getm.xml |
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| diff -r 7e6f943984b0 -r 1e048d0cda1d minfi_getm.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_getm.xml Fri Feb 22 08:13:51 2019 -0500 |
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| @@ -0,0 +1,41 @@ +<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> + |