Mercurial > repos > testtool > get_gr_set

comparison GRsetFromGEO/GRsetFromGEO.xml @ 30:4f157ee63207 draft

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author testtool
date Mon, 10 Jul 2017 10:24:07 -0400
parents 5d796e9a96ae
children b61aac190ca6
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29:5d796e9a96ae 30:4f157ee63207
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"