comparison GRsetFromGEO/GRsetFromGEO.xml @ 12:0631845b906d draft

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author testtool
date Wed, 12 Apr 2017 08:29:45 -0400
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11:983651783ce9 12:0631845b906d
1 <tool id="GRset" name="GRsetFromGEO" version="1.16.2">
2 <requirements>
3 <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
9 <inputs>
10 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
11 </inputs>
12 <outputs>
13 <data format="Rdata" name="output" label="GenomicRatioSet.Rdata"/>
14 </outputs>
15 <tests>
16 <test>
17 <param name="test">
18 <element name="test-data">
19 <collection type="data">
20 <element name="GSE" value="GSE51547"/>
21 </collection>
22 </element>
23 </param>
24 <output format="Rdata" name="output" label="test-data/GenomicRatioSet.Rdata"/>
25 </test>
26 </tests>
27 <help>
28 Reading Illumina methylation array data from GEO.
29 </help>
30 <citations>
31 Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369.
32 </citations>
33 </tool>