Mercurial > repos > kpbioteam > ewastools
annotate minfi_maptogenome.xml @ 75:9c6fbb7d5a2a draft
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
| author | kpbioteam |
|---|---|
| date | Mon, 20 May 2019 07:14:26 -0400 |
| parents | ea20cc034d53 |
| children |
| rev | line source |
|---|---|
| 67 | 1 <tool id="minfi_maptogenome" name="Minfi Map to Genome" version="@MINFI_VERSION@"> |
| 10 | 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 '$minfi_mtg_script' | |
| 12 ]]> | |
| 13 </command> | |
| 14 <configfiles> | |
|
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
67
diff
changeset
|
15 <configfile name="minfi_mtg_script"><![CDATA[ |
| 10 | 16 require("minfi", quietly = TRUE) |
| 17 require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE) | |
| 18 | |
| 19 RSet <- get(load('$rset')) | |
| 20 | |
| 21 GRSet <- mapToGenome(RSet) | |
| 22 | |
| 23 save(GRSet,file = '$grset') | |
| 24 ]]> | |
|
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
67
diff
changeset
|
25 </configfile> |
| 10 | 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> |