Mercurial > repos > kpbioteam > ewastools
annotate minfi_getsnp.xml @ 76:fef50103f6b3 draft
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
| author | kpbioteam |
|---|---|
| date | Fri, 07 Jun 2019 08:57:26 -0400 |
| parents | 9c6fbb7d5a2a |
| children |
| rev | line source |
|---|---|
| 73 | 1 <tool id="minfi_getsnp" name="Minfi Get SNPs" version="@MINFI_VERSION@"> |
| 11 | 2 <description>retrieve the chromosome and the position of each SNP</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 '$minfi_snp_script' | |
| 12 ]]> | |
| 13 </command> | |
| 14 <configfiles> | |
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9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
73
diff
changeset
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15 <configfile name="minfi_snp_script"><![CDATA[ |
| 11 | 16 require("minfi", quietly = TRUE) |
| 17 | |
| 18 GRSet <- get(load('$grset')) | |
| 19 | |
| 20 snps <- getSnpInfo(GRSet) | |
| 21 | |
| 22 write.table(snps, '$table') | |
| 23 ]]> | |
|
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
73
diff
changeset
|
24 </configfile> |
| 11 | 25 </configfiles> |
|
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
73
diff
changeset
|
26 <inputs> |
|
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
73
diff
changeset
|
27 <param type="data" name="grset" format="rdata" label="Data Mapped To The Genome" |
|
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
73
diff
changeset
|
28 help="This class (GenomicRatioSet) holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/> |
| 11 | 29 </inputs> |
| 30 <outputs> | |
| 31 <data name="table" format="txt" label="SNPInfo Table"/> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="grset" value="GRSet.rdata"/> | |
| 36 <output name="table" file="SNPInfo_Table.txt"/> | |
| 37 </test> | |
| 38 </tests> | |
| 39 <help><![CDATA[ | |
| 40 This tool is a version of the getSnpInfo adapted to retrieve the chromosome and the position of each SNP on a given Affymetrix SNP Array. | |
| 41 ]]></help> | |
| 42 <expand macro="citations" /> | |
| 43 </tool> | |
| 44 |