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comparison getGRsetFromGEO/getGRsetFromGEO.xml @ 0:457c1fc71f64 draft

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author testtool
date Sun, 11 Jun 2017 06:21:37 -0400
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1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="getGRsetFromGEO" name="getGRsetFromGEO" version="1.18.4">
3 <requirements>
4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
10 <inputs>
11 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
12 </inputs>
13 <outputs>
14 <data format="RDdata" name="output" label="GRsetFromGEO.RData"/>
15 </outputs>
16 <tests>
17 <test>
18 <param name="test">
19 <element name="test-data">
20 <collection type="data">
21 <element name="GSE" value="GSE51547"/>
22 </collection>
23 </element>
24 </param>
25 <output type="data" format="RData" name="output" label="test-data/out.RData"/>
26 </test>
27 </tests>
28 <help>
29 **What it does**
30 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
31 **Input**
32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
33 **Output**
34 GenomicRatioSet object
35 </help>
36 <citations>
37 <citation type="doi">10.1093/bioinformatics/btu049</citation>
38 </citations>
39 </tool>