Mercurial > repos > kpbioteam > minfi_ppnoob
changeset 0:a003221d59cc draft default tip
planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty
| author | kpbioteam |
|---|---|
| date | Sun, 11 Feb 2018 08:28:49 -0500 |
| parents | |
| children | |
| files | RGSet.rdata minfi_ppnoob.R minfi_ppnoob.xml noob.rdata test-data/RGSet.rdata test-data/noob.rdata |
| diffstat | 6 files changed, 41 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_ppnoob.R Sun Feb 11 08:28:49 2018 -0500 @@ -0,0 +1,12 @@ +require("minfi", quietly = TRUE) + +args <- commandArgs(trailingOnly = TRUE) + +input = args[1] +output = args[2] + +RGSet <- get(load(input)) + +MSet <- preprocessNoob(RGSet) + +save(MSet,file = output)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_ppnoob.xml Sun Feb 11 08:28:49 2018 -0500 @@ -0,0 +1,29 @@ +<tool id="minfi_ppnoob" name="minfi_ppnoob" version="0.1.0"> + <description>implements the noob background subtraction method with dye-bias normalization</description> + <requirements> + <requirement type="package" version="1.24.0">bioconductor-minfi</requirement> + <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation450kmanifest</requirement> + <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript ${__tool_directory__}/minfi_ppnoob.R "$input1" "$output1" + ]]></command> + <inputs> + <param type="data" name="input1" format="rdata" /> + </inputs> + <outputs> + <data name="output1" format="rdata" /> + </outputs> + <tests> + <test> + <param name="input1" value="RGSet.rdata"/> + <output name="output1" file="noob.rdata"/> + </test> + </tests> + <help><![CDATA[ + Background subtraction method estimates background noise from the out-of-band probes and remove it for each sample separately, while the dye-bias normalization utilizes a subset of the control probes to estimate the dye bias. + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu049</citation> + </citations> +</tool> \ No newline at end of file