Mercurial > repos > kpbioteam > ewastools
view minfi_qc.xml @ 74:53aaf097238c draft
planemo upload commit b4d745c28290bce5c7653886d70a63b001aaab19-dirty
author | kpbioteam |
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date | Thu, 16 May 2019 08:56:35 -0400 |
parents | a1320b7a6d52 |
children | 9c6fbb7d5a2a |
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<tool id="minfi_qc" name="Minfi QC" version="@MINFI_VERSION@"> <description>provides a simple quality control matrix and plot</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ Rscript '$read_qc_script' ]]> </command> <configfiles> <configfile name="read_qc_script"> <![CDATA[ require("minfi", quietly = TRUE) MSet <- get(load('$MethylSet')) qc <- getQC(MSet) write.table(qc, '$qctab') png('$qcpng') plotQC(qc) dev.off() ]]> </configfile> </configfiles> <inputs> <param type="data" name="MethylSet" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/> </inputs> <outputs> <data name="qctab" format="txt" label="Quality Control Report"/> <data name="qcpng" format="png" label="Quality Control Plot"/> </outputs> <tests> <test> <param name="MethylSet" value="MethylSet.rdata"/> <output name="qctab" file="Quality_Control_Report.txt"/> <output name="qcpng" file="Quality_Control_Plot.png" compare="sim_size"/> </test> </tests> <help><![CDATA[ Quality Control (QC) outputs plot of the log median intensity in both the methylated (M) and unmethylated (U) channels. When plotting these two medians against each other the good samples cluster together, while failed samples tend to separate and have lower median intensities. ]]></help> <expand macro="citations" /> </tool>