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comparison GRsetFromGEO/GRsetFromGEO.xml @ 61:2382697aad09 draft

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author testtool
date Thu, 11 Jan 2018 12:48:29 -0500
parents dc0d9276a8f1
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60:dc0d9276a8f1 61:2382697aad09
1 <tool id="getGRset" name="GRsetFromGEO"> 1 <tool id="getGRset" name="GRsetFromGEO" version="1.0.0">
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 <command detect_errors="aggressive"> 7 <command detect_errors="aggressive">
8 Rscript '$__tool_directory__/GRsetFromGEO.R' '$input' '$output' 8 Rscript '$__tool_directory__/GRsetFromGEO.R' '$input' '$output'
9 </command> 9 </command>
10 <inputs> 10 <inputs>
11 <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> 11 <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE42752'"/>
12 </inputs> 12 </inputs>
13 <outputs> 13 <outputs>
14 <data format="rdata" name="output" label="output.rdata" /> 14 <data format="rdata" name="output" label="output.rdata" />
15 </outputs> 15 </outputs>
16 <help> 16 <tests>
17 **What it does** 17 <test>
18 18 <param name="input" value="GSE42752"/>
19 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object 19 <output name="output" file="out.rdata"/>
20 20 </test>
21 **Input** 21 </tests>
22 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" 22 <help>
23 23 **What it does**
24 **Output** 24
25 GenomicRatioSet object 25 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
26 </help> 26
27 **Input**
28 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
29
30 **Output**
31 GenomicRatioSet object
32 </help>
33 <citations>
34 <citation type="doi">10.1093/bioinformatics/btm254</citation>
35 <citation type="doi">10.1093/bioinformatics/btu049</citation>
36 </citations>
27 </tool> 37 </tool>