Mercurial > repos > testtool > get_gr_set
changeset 61:2382697aad09 draft
Uploaded
| author | testtool |
|---|---|
| date | Thu, 11 Jan 2018 12:48:29 -0500 |
| parents | dc0d9276a8f1 |
| children | 8673a0225e2b |
| files | GRsetFromGEO/._GRsetFromGEO.xml GRsetFromGEO/._~$setFromGEO.xml GRsetFromGEO/GRsetFromGEO.R GRsetFromGEO/GRsetFromGEO.xml GRsetFromGEO/test-data/._.DS_Store GRsetFromGEO/test-data/out.RData GRsetFromGEO/test-data/out.rdata GRsetFromGEO/~$setFromGEO.xml |
| diffstat | 8 files changed, 28 insertions(+), 15 deletions(-) [+] |
line wrap: on
line diff
--- a/GRsetFromGEO/GRsetFromGEO.R Wed Sep 06 06:02:44 2017 -0400 +++ b/GRsetFromGEO/GRsetFromGEO.R Thu Jan 11 12:48:29 2018 -0500 @@ -1,4 +1,8 @@ require(minfi, quietly = TRUE) +require(IlluminaHumanMethylation450kanno.ilmn12.hg19, quietly = TRUE) + +options('GEOquery.inmemory.gpl'=TRUE) +options('download.file.method.GEOquery' = 'libcurl') options(warn = -1) @@ -8,6 +12,5 @@ GRset <- getGenomicRatioSetFromGEO(input) -save(GRset,file = output) +save(GRset, file = output) -
--- a/GRsetFromGEO/GRsetFromGEO.xml Wed Sep 06 06:02:44 2017 -0400 +++ b/GRsetFromGEO/GRsetFromGEO.xml Thu Jan 11 12:48:29 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="getGRset" name="GRsetFromGEO"> +<tool id="getGRset" name="GRsetFromGEO" version="1.0.0"> <description>downloads data from GEO</description> <requirements> <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> @@ -8,20 +8,30 @@ 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'"/> + <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE42752'"/> </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> + <tests> + <test> + <param name="input" value="GSE42752"/> + <output name="output" file="out.rdata"/> + </test> + </tests> + <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> + <citations> + <citation type="doi">10.1093/bioinformatics/btm254</citation> + <citation type="doi">10.1093/bioinformatics/btu049</citation> + </citations> </tool>