|
12
|
1 <tool id="GRset" name="GRsetFromGEO" version="1.16.2">
|
|
|
2 <requirements>
|
|
32
|
3 <requirement type="package" version="3.2.1">R</requirement>
|
|
|
4 </requirements>
|
|
12
|
5 <stdio>
|
|
|
6 <exit_code range="1:" />
|
|
|
7 </stdio>
|
|
|
8 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
|
|
|
9 <inputs>
|
|
29
|
10 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
|
|
12
|
11 </inputs>
|
|
|
12 <outputs>
|
|
32
|
13 <data format="txt" name="output" label="GSMTable.txt"/>
|
|
12
|
14 </outputs>
|
|
|
15 <tests>
|
|
|
16 <test>
|
|
|
17 <param name="test">
|
|
|
18 <element name="test-data">
|
|
29
|
19 <collection type="data">
|
|
12
|
20 <element name="GSE" value="GSE51547"/>
|
|
|
21 </collection>
|
|
|
22 </element>
|
|
|
23 </param>
|
|
32
|
24 <output format="txt" name="output" label="test-data/GSMTable.txt"/>
|
|
12
|
25 </test>
|
|
|
26 </tests>
|
|
|
27 <help>
|
|
31
|
28 Reading Illumina methylation array data from GEO.
|
|
12
|
29 </help>
|
|
|
30 <citations>
|
|
31
|
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.
|
|
12
|
32 </citations>
|
|
|
33 </tool>
|
