Mercurial > repos > kpbioteam > ewastools
annotate minfi_dropsnp.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 | 5cda2c8d0316 |
| children |
| rev | line source |
|---|---|
| 65 | 1 <tool id="minfi_dropsnp" name="Minfi Drop SNPs" version="@MINFI_VERSION@"> |
| 15 | 2 <description>drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension</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 '$minfi_snp_script' | |
| 12 ]]> | |
| 13 </command> | |
| 14 <configfiles> | |
| 15 <configfile name="minfi_snp_script"><![CDATA[ | |
| 16 require("minfi", quietly = TRUE) | |
| 17 | |
| 18 GRSet <- get(load('$grset')) | |
| 19 | |
| 20 GRSet <- dropLociWithSnps(GRSet, snps=c("SBE","CpG"), maf=0) | |
| 21 | |
| 22 save(GRSet,file = '$grsetwithoutsnp') | |
| 23 ]]> | |
| 24 </configfile> | |
| 25 </configfiles> | |
| 26 <inputs> | |
|
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
72
diff
changeset
|
27 <param type="data" name="grset" format="rdata" label="Genomic Ratio Set" |
|
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
72
diff
changeset
|
28 help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/> |
| 15 | 29 </inputs> |
| 30 <outputs> | |
| 72 | 31 <data name="grsetwithoutsnp" format="rdata" from_work_dir="dropsnpGRSet.rdata" label="Data Mapped To The Genome without SNPs"/> |
| 15 | 32 </outputs> |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="grset" value="GRSet.rdata"/> | |
| 36 <output name="grsetwithoutsnp" file="GRSet_without_SNPs.rdata"/> | |
| 37 </test> | |
| 38 </tests> | |
| 39 <help><![CDATA[ | |
| 40 This tool is a version of the dropLociWithSnps function adapted to drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension (recommend). | |
| 41 | |
| 42 The output is a GenomicRatioSet object without SNPs loci. | |
| 43 ]]></help> | |
| 44 <expand macro="citations" /> | |
| 45 </tool> |