Mercurial > repos > kpbioteam > ewastools
comparison minfi_qc.xml @ 6:4f34e3f73ebf draft
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| author | kpbioteam |
|---|---|
| date | Fri, 22 Feb 2019 08:11:45 -0500 |
| parents | |
| children | a1320b7a6d52 |
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| 5:ab6e72fdf350 | 6:4f34e3f73ebf |
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| 1 <tool id="minfi_qc" name="Minfi qc" version="@MINFI_VERSION@"> | |
| 2 <description>provides a simple quality control matrix and plot</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"> | |
| 8 <![CDATA[ | |
| 9 Rscript '$read_qc_script' | |
| 10 ]]> | |
| 11 </command> | |
| 12 <configfiles> | |
| 13 <configfile name="read_qc_script"> | |
| 14 <![CDATA[ | |
| 15 require("minfi", quietly = TRUE) | |
| 16 | |
| 17 MSet <- get(load('$MethylSet')) | |
| 18 | |
| 19 qc <- getQC(MSet) | |
| 20 | |
| 21 write.table(qc, '$qctab') | |
| 22 | |
| 23 png('$qcpng') | |
| 24 plotQC(qc) | |
| 25 dev.off() | |
| 26 ]]> | |
| 27 </configfile> | |
| 28 </configfiles> | |
| 29 <inputs> | |
| 30 <param type="data" name="MethylSet" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic | |
| 31 location."/> | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data name="qctab" format="txt" label="Quality Control Report"/> | |
| 35 <data name="qcpng" format="png" label="Quality Control Plot"/> | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="MethylSet" value="MethylSet.rdata"/> | |
| 40 <output name="qctab" file="Quality_Control_Report.txt"/> | |
| 41 <output name="qcpng" file="Quality_Control_Plot.png" compare="sim_size"/> | |
| 42 </test> | |
| 43 </tests> | |
| 44 <help><![CDATA[ | |
| 45 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. | |
| 46 ]]></help> | |
| 47 <expand macro="citations" /> | |
| 48 </tool> |