Mercurial > repos > testtool > get_gr_set

comparison GRsetFromGEO/GRsetFromGEO.xml @ 6:3cd5fb747251 draft

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author testtool
date Sun, 11 Jun 2017 08:00:36 -0400
parents 7511130b5068
children bfc8b961afe1
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5:7511130b5068 6:3cd5fb747251
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="GetGEO" name="GRsetFromGEO" version="1.16.2"> 2 <tool id="GetGEO" name="GRsetFromGEO" version="1.16.2">
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 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> 9 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
10 <inputs> 10 <inputs>
11 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> 11 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
12 </inputs> 12 </inputs>
24 </param> 24 </param>
25 <output type="data" format="RData" name="output" label="test-data/out.RData"/> 25 <output type="data" format="RData" name="output" label="test-data/out.RData"/>
26 </test> 26 </test>
27 </tests> 27 </tests>
28 <help> 28 <help>
29 **What it does** 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 30 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
31 **Input** 31 **Input**
32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" 32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
33 **Output** 33 **Output**
34 GenomicRatioSet object 34 GenomicRatioSet object
35 </help> 35 </help>
36 <citations> 36 <citations>
37 <citation type="doi">10.1093/bioinformatics/btu049</citation> 37 <citation type="doi">10.1093/bioinformatics/btu049</citation>
38 </citations> 38 </citations>
39 </tool> 39 </tool>