Mercurial > repos > testtool > get_gr_set
comparison GRsetFromGEO/GRsetFromGEO.xml @ 30:4f157ee63207 draft
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author | testtool |
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date | Mon, 10 Jul 2017 10:24:07 -0400 |
parents | 5d796e9a96ae |
children | b61aac190ca6 |
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29:5d796e9a96ae | 30:4f157ee63207 |
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1 <?xml version="1.0" encoding="UTF-8"?> | 1 <tool id="getGRset" name="GRsetFromGEO"> |
2 <tool id="GetGEO" name="GRsetFromGEO" version="1.16.2"> | 2 <description>downloads data from GEO</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> | 4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> |
5 </requirements> | 5 <requirement type="package" version="0.2.1">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> |
6 <stdio> | 6 </requirements> |
7 <exit_code range="1:" /> | 7 <stdio> |
8 </stdio> | 8 <exit_code range="1:" /> |
9 </stdio> | |
9 <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command> | 10 <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command> |
10 <inputs> | 11 <inputs> |
11 <param name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> | 12 <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> |
12 </inputs> | 13 </inputs> |
13 <outputs> | 14 <outputs> |
14 <data format="RDdata" name="output" label="GRsetFromGEO.RData"/> | 15 <data format="RDdata" name="output" label="output.RData" /> |
15 </outputs> | 16 </outputs> |
16 <tests> | |
17 <test> | |
18 <param name="test"> | |
19 <element name="test-data"> | |
20 <collection type="data"> | |
21 <element name="input" 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> | 17 <help> |
29 **What it does** | 18 **What it does** |
30 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object | 19 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object |
31 **Input** | 20 **Input** |
32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" | 21 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" |
33 **Output** | 22 **Output** |
34 GenomicRatioSet object | 23 GenomicRatioSet object |
35 </help> | 24 </help> |
36 <citations> | |
37 <citation type="doi">10.1093/bioinformatics/btu049</citation> | |
38 </citations> | |
39 </tool> | 25 </tool> |
26 Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output" |