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comparison GRsetFromGEO/GRsetFromGEO.xml @ 60:dc0d9276a8f1 draft

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author testtool
date Wed, 06 Sep 2017 06:02:44 -0400
parents c356d89b0145
children 2382697aad09
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59:c356d89b0145 60:dc0d9276a8f1
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 <command detect_errors="aggressive">
8 <exit_code range="1:" /> 8 Rscript '$__tool_directory__/GRsetFromGEO.R' '$input' '$output'
9 </stdio> 9 </command>
10 <command>Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output"</command> 10 <inputs>
11 <inputs> 11 <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'"/> 12 </inputs>
13 </inputs> 13 <outputs>
14 <outputs> 14 <data format="rdata" name="output" label="output.rdata" />
15 <data format="rdata" name="output" label="output.rdata" /> 15 </outputs>
16 </outputs> 16 <help>
17 <help>
18 **What it does** 17 **What it does**
18
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
20 **Input** 21 **Input**
21 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" 22 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
23
22 **Output** 24 **Output**
23 GenomicRatioSet object 25 GenomicRatioSet object
24 </help> 26 </help>
25 </tool> 27 </tool>