Mercurial > repos > kpbioteam > ewastools
comparison minfi_mset.xml @ 9:3511473319c2 draft
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| author | kpbioteam |
|---|---|
| date | Fri, 22 Feb 2019 08:12:46 -0500 |
| parents | |
| children | 53aaf097238c |
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| 8:432fd69157fa | 9:3511473319c2 |
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| 1 <tool id="minfi_mset" name="Minfi mset" version="@MINFI_VERSION@"> | |
| 2 <description>Create objects contains CpGs signals</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"> | |
| 8 <![CDATA[ | |
| 9 Rscript '$minfi_mset_script' | |
| 10 ]]> | |
| 11 </command> | |
| 12 <configfiles> | |
| 13 <configfile name="minfi_mset_script"><![CDATA[ | |
| 14 require("minfi", quietly = TRUE) | |
| 15 | |
| 16 RGSet <- get(load('$RGChannelSet')) | |
| 17 | |
| 18 MSet <- preprocessRaw(RGSet) | |
| 19 | |
| 20 save(MSet,file = '$MethylSet') | |
| 21 | |
| 22 ]]> | |
| 23 </configfile> | |
| 24 </configfiles> | |
| 25 <inputs> | |
| 26 <param type="data" name="RGChannelSet" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array."/> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data name="MethylSet" format="rdata" label="MethylSet" /> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="RGChannelSet" value="RGChannelSet.rdata"/> | |
| 34 <output name="MethylSet" file="MethylSet.rdata"/> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help><![CDATA[ | |
| 38 This tool is transforming a class representing raw (unprocessed) data from a two color micro array - RGChannelSet into a class holding preprocessed data for Illumina methylation microarrays, mapped to genomic location - MethylSet. | |
| 39 ]]></help> | |
| 40 <expand macro="citations" /> | |
| 41 </tool> |