Mercurial > repos > testtool > get_gr_set
changeset 18:25490621d43e draft
Uploaded
| author | testtool |
|---|---|
| date | Mon, 03 Jul 2017 07:13:38 -0400 |
| parents | 3431c6054674 |
| children | 0a619d0e45fd |
| files | GRsetFromGEO.xml |
| diffstat | 1 files changed, 39 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO.xml Mon Jul 03 07:13:38 2017 -0400 @@ -0,0 +1,39 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="GetGEO" name="GRsetFromGEO" version="1.16.2"> +<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 name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> + </inputs> + <outputs> + <data format="RDdata" name="output" label="GRsetFromGEO.RData"/> + </outputs> + <tests> + <test> + <param name="test"> + <element name="test-data"> + <collection type="data"> + <element name="input" value="GSE51547"/> + </collection> + </element> + </param> + <output type="data" format="RData" name="output" label="test-data/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/btu049</citation> + </citations> +</tool>