comparison minfi_rset.xml @ 4:8a3d5d8a433f draft

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author kpbioteam
date Fri, 22 Feb 2019 08:10:56 -0500
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children 297a0cda5c7b
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3:5549088d4c65 4:8a3d5d8a433f
1 <tool id="minfi_rset" name="Minfi rset" version="@MINFI_VERSION@">
2 <description>store Beta values and/or M values</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 Rscript '$read_rset_script'
10 ]]>
11 </command>
12 <configfiles>
13 <configfile name="read_rset_script">
14 <![CDATA[
15 require("minfi", quietly = TRUE)
16 MSet <- get(load('$mset'))
17
18 RSet <- ratioConvert(MSet, what = "both", keepCN = TRUE)
19
20 save(RSet,file = '$rset')
21 ]]> </configfile>
22 </configfiles>
23 <inputs>
24 <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
25 location."/>
26 </inputs>
27 <outputs>
28 <data name="rset" format="rdata" label="RatioSet"/>
29 </outputs>
30 <tests>
31 <test>
32 <param name="mset" value="MethylSet.rdata"/>
33 <output name="rset" file="RatioSet.rdata"/>
34 </test>
35 </tests>
36 <help><![CDATA[
37 RSet class holds preprocessed data for Illumina methylation microarrays. It contains respectively the Beta value matrix, M value matrix and the Copy Number matrix.
38 ]]></help>
39 <expand macro="citations" />
40 </tool>