Mercurial > repos > kpbioteam > ewastools
view minfi_getm.xml @ 76:fef50103f6b3 draft
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
author | kpbioteam |
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date | Fri, 07 Jun 2019 08:57:26 -0400 |
parents | 9c6fbb7d5a2a |
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<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>