|
30
|
1 <tool id="getGRset" name="GRsetFromGEO">
|
|
|
2 <description>downloads data from GEO</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
|
|
35
|
5 <requirement type="package" version="0.6.0">'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19'</requirement>
|
|
30
|
6 </requirements>
|
|
|
7 <stdio>
|
|
|
8 <exit_code range="1:" />
|
|
|
9 </stdio>
|
|
27
|
10 <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command>
|
|
20
|
11 <inputs>
|
|
30
|
12 <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
|
|
20
|
13 </inputs>
|
|
|
14 <outputs>
|
|
30
|
15 <data format="RDdata" name="output" label="output.RData" />
|
|
20
|
16 </outputs>
|
|
|
17 <help>
|
|
30
|
18 **What it does**
|
|
|
19 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
|
|
|
20 **Input**
|
|
|
21 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
|
|
|
22 **Output**
|
|
|
23 GenomicRatioSet object
|
|
20
|
24 </help>
|
|
5
|
25 </tool>
|
|
30
|
26 Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output"
|
