Mercurial > repos > testtool > get_gr_set

comparison GRsetFromGEO/GRsetFromGEO.xml @ 40:343324c86875 draft

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author testtool
date Mon, 07 Aug 2017 09:59:58 -0400
parents 10996f6ddcb5
children 3ee5ebb721ad
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39:05f6acc80f47 40:343324c86875
1 <tool id="getGRset" name="GRsetFromGEO"> 1 <tool id="getGRset" name="GRsetFromGEO">
2 <description>downloads data from GEO</description> 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 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> 5 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 </stdio> 9 </stdio>
10 <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command> 10 <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.rdata</command>
11 <inputs> 11 <inputs>
12 <param format="text" 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'"/>
13 </inputs> 13 </inputs>
14 <outputs> 14 <outputs>
15 <data format="RDdata" name="output" label="output.RData" /> 15 <data format="rdata" name="output" label="output.rdata" />
16 </outputs> 16 </outputs>
17 <help> 17 <help>
18 **What it does** 18 **What it does**
19 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
20 **Input** 20 **Input**