Mercurial > repos > testtool > geo_data
comparison GRsetFromGEO/GRsetFromGEO.xml @ 27:2d4a97506931 draft
Uploaded
| 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> |