comparison minfi_getbeta.xml @ 14:8833eedd24fb draft

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author kpbioteam
date Fri, 22 Feb 2019 08:14:44 -0500
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children 9c6fbb7d5a2a
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13:db44217b3c5d 14:8833eedd24fb
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>