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comparison minfi_maptogenome.xml @ 10:7d6e9bd197b8 draft

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author kpbioteam
date Fri, 22 Feb 2019 08:13:15 -0500
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9:3511473319c2 10:7d6e9bd197b8
1 <tool id="minfi_maptogenome" name="Minfi map to genome" version="@MINFI_VERSION@">
2 <description>mapping Ilumina methylation array data to the genome</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
8 </expand>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 Rscript '$minfi_mtg_script'
12 ]]>
13 </command>
14 <configfiles>
15 <configfile name="minfi_mtg_script"><![CDATA[
16 require("minfi", quietly = TRUE)
17 require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
18
19 RSet <- get(load('$rset'))
20
21 GRSet <- mapToGenome(RSet)
22
23 save(GRSet,file = '$grset')
24 ]]>
25 </configfile>
26 </configfiles>
27 <inputs>
28 <param type="data" name="rset" format="rdata" label="Methylation Data to Map" help="This class holds preprocessed data for Illumina methylation microarrays." />
29 </inputs>
30 <outputs>
31 <data name="grset" format="rdata" from_work_dir="GRSet.rdata" label= "Data Mapped To The Genome" />
32 </outputs>
33 <tests>
34 <test>
35 <param name="rset" value="RatioSet.rdata"/>
36 <output name="grset" file="GRSet.rdata"/>
37 </test>
38 </tests>
39 <help><![CDATA[
40 This tool is mapping Ilumina methylation array data to the genome using 450k annotation package. Depending on the genome, not all methylation loci may have a genomic position. The output is an a GenomicRatioSet object.
41 ]]></help>
42 <expand macro="citations" />
43 </tool>