Mercurial > repos > testtool > get_gr_set
view GRsetFromGEO/GRsetFromGEO.xml @ 7:c31140daf71f draft
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author | testtool |
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date | Mon, 12 Jun 2017 11:44:26 -0400 |
parents | 3cd5fb747251 |
children | bfc8b961afe1 |
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<?xml version="1.0" encoding="UTF-8"?> <tool id="GetGEO" name="GRsetFromGEO" version="1.16.2"> <requirements> <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> <inputs> <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> </inputs> <outputs> <data format="RDdata" name="output" label="GRsetFromGEO.RData"/> </outputs> <tests> <test> <param name="test"> <element name="test-data"> <collection type="data"> <element name="GSE" value="GSE51547"/> </collection> </element> </param> <output type="data" format="RData" name="output" label="test-data/out.RData"/> </test> </tests> <help> **What it does** This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object **Input** The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" **Output** GenomicRatioSet object </help> <citations> <citation type="doi">10.1093/bioinformatics/btu049</citation> </citations> </tool>