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comparison GRsetFromGEO/GRsetFromGEO.xml @ 27:2d4a97506931 draft

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author testtool
date Thu, 13 Apr 2017 11:01:46 -0400
parents c7bab1a516ce
children 3d281ad15b83
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26:c7bab1a516ce 27:2d4a97506931
1 <tool id="GRset" name="GRsetFromGEO" version="1.16.2"> 1 <tool id="GRset" name="GRsetFromGEO" version="1.16.2">
2 <description>
3 Reading Illumina methylation array data from GEO.
4 </description>
2 <requirements> 5 <requirements>
3 <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement> 6 <requirement type="package" version="3.2.1">R</requirement>
4 </requirements> 7 </requirements>
5 <stdio> 8 <stdio>
6 <exit_code range="1:" /> 9 <exit_code range="1:" />
7 </stdio> 10 </stdio>
8 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> 11 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
9 <inputs> 12 <inputs>
10 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> 13 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
11 </inputs> 14 </inputs>
12 <outputs> 15 <outputs>
13 <data format="RData" name="output" label="GenomicRatioSet.Rdata"/> 16 <data format="RData" name="output" label="GenomicRatioSet.RData"/>
14 </outputs> 17 </outputs>
15 <tests> 18 <tests>
16 <test> 19 <test>
17 <param name="test"> 20 <param name="test">
18 <element name="test-data"> 21 <element name="test-data">
19 <collection type="data"> 22 <collection type="data">
20 <element name="GSE" value="GSE51547"/> 23 <element name="GSE" value="GSE51547"/>
21 </collection> 24 </collection>
22 </element> 25 </element>
23 </param> 26 </param>
24 <output format="RData" name="output" label="test-data/GenomicRatioSet.Rdata"/> 27 <output format="RData" name="output" label="test-data/GenomicRatioSet.RData"/>
25 </test> 28 </test>
26 </tests> 29 </tests>
27 <help> 30 <help>
28 Reading Illumina methylation array data from GEO. 31 Reading Illumina methylation array data from GEO.
29 </help> 32 </help>
30 <citations> 33 <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. 34 Aryee, Martin J, et al "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays" Bioinformatics 3010 (2014): 1363-1369
32 </citations> 35 </citations>
33 </tool> 36 </tool>