Mercurial > repos > kpbioteam > ewastools
comparison minfi_getbeta.xml @ 14:8833eedd24fb draft
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| author | kpbioteam |
|---|---|
| date | Fri, 22 Feb 2019 08:14:44 -0500 |
| parents | |
| children | 9c6fbb7d5a2a |
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| 13:db44217b3c5d | 14:8833eedd24fb |
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| 1 <tool id="minfi_getbeta" name="Minfi Get Beta" version="@MINFI_VERSION@"> | |
| 2 <description>obtain Beta value matrix</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"> | |
| 8 <![CDATA[ | |
| 9 Rscript '$minfi_beta_script' | |
| 10 ]]> | |
| 11 </command> | |
| 12 <configfiles> | |
| 13 <configfile name="minfi_beta_script"><![CDATA[ | |
| 14 require("minfi", quietly = TRUE) | |
| 15 | |
| 16 MSet <- get(load('$mset')) | |
| 17 | |
| 18 beta <- getBeta(MSet) | |
| 19 | |
| 20 write.table(beta, file = '$matrix', quote = FALSE, sep = "\t") | |
| 21 ]]> | |
| 22 </configfile> | |
| 23 </configfiles> | |
| 24 <inputs> | |
| 25 <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic | |
| 26 location."/> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data name="matrix" format="bedgraph" label="Beta Values Matrix"/> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="mset" value="MethylSet.rdata"/> | |
| 34 <output name="matrix" file="Beta_Values_Matrix.bedgraph"/> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help><![CDATA[ | |
| 38 This tools outputs an interval file of methylation indices (beta values), which are continuous values between 0 and 1 representing the ratio/fraction of the intensity of the methylated-probe signal to the total signal intensity for each probed CpG site. | |
| 39 ]]></help> | |
| 40 <expand macro="citations" /> | |
| 41 </tool> |