Mercurial > repos > testtool > get_gr_set
changeset 53:5547aeb4ff23 draft
Deleted selected files
| author | testtool |
|---|---|
| date | Thu, 10 Aug 2017 06:19:48 -0400 |
| parents | d6c7c3ed3290 |
| children | 5752f23e451f |
| files | GRsetFromGEO/test-data/GRsetFromGEO.R GRsetFromGEO/test-data/GRsetFromGEO.xml |
| diffstat | 2 files changed, 0 insertions(+), 40 deletions(-) [+] |
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--- a/GRsetFromGEO/test-data/GRsetFromGEO.R Thu Aug 10 06:19:36 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -require(minfi, quietly = TRUE) - -options(warn = -1) -options('download.file.method.GEOquery' = 'wget') -options('GEOquery.inmemory.gpl'=FALSE) - - -args <- commandArgs(trailingOnly = TRUE) -input = args[1] -output = args[2] - -GRset <- getGenomicRatioSetFromGEO(input) - -save(GRset,file = output) - -
--- a/GRsetFromGEO/test-data/GRsetFromGEO.xml Thu Aug 10 06:19:36 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -<tool id="getGRset" name="GRsetFromGEO"> - <description>downloads data from GEO</description> - <requirements> -<requirement type="package" version="1.20.0">bioconductor-minfi</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command>Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output"</command> - <inputs> - <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> - </inputs> - <outputs> - <data format="rdata" name="output" label="output.rdata" /> - </outputs> - <help> - **What it does** - This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object - **Input** - The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" - **Output** - GenomicRatioSet object - </help> -</tool>