Mercurial > repos > testtool > get_gr_set

comparison GRsetFromGEO/GRsetFromGEO.xml @ 27:d492a31c50f1 draft

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author testtool
date Mon, 10 Jul 2017 08:58:44 -0400
parents 40d7bdac6322
children ab34c2e8e533
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26:b003e02d1ea4 27:d492a31c50f1
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 <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command>
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 $__tool_directory__/GRsetFromGEO.R "$input" "$output" </command>
10 <inputs> 4 <inputs>
11 <param name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> 5 <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
12 </inputs> 6 </inputs>
13 <outputs> 7 <outputs>
14 <data format="RDdata" name="output" label="GRsetFromGEO.RData"/> 8 <data format="RDdata" name="output" label="output.RData" />
15 </outputs> 9 </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> 10 <help>
29 **What it does** 11 **What it does**
30 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object 12 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
31 **Input** 13 **Input**
32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" 14 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
33 **Output** 15 **Output**
34 GenomicRatioSet object 16 GenomicRatioSet object
35 </help> 17 </help>
36 <citations>
37 <citation type="doi">10.1093/bioinformatics/btu049</citation>
38 </citations>
39 </tool> 18 </tool>