Mercurial > repos > testtool > get_gr_set
comparison getGRsetFromGEO/getGRsetFromGEO.xml @ 0:457c1fc71f64 draft
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author | testtool |
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date | Sun, 11 Jun 2017 06:21:37 -0400 |
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-1:000000000000 | 0:457c1fc71f64 |
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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> |