Mercurial > repos > testtool > get_gr_set
comparison GRsetFromGEO/GRsetFromGEO.xml @ 6:3cd5fb747251 draft
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| author | testtool |
|---|---|
| date | Sun, 11 Jun 2017 08:00:36 -0400 |
| parents | 7511130b5068 |
| children | bfc8b961afe1 |
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| 5:7511130b5068 | 6:3cd5fb747251 |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 2 <tool id="GetGEO" name="GRsetFromGEO" version="1.16.2"> | 2 <tool id="GetGEO" name="GRsetFromGEO" version="1.16.2"> |
| 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 </requirements> | 5 </requirements> |
| 6 <stdio> | 6 <stdio> |
| 7 <exit_code range="1:" /> | 7 <exit_code range="1:" /> |
| 8 </stdio> | 8 </stdio> |
| 9 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> | 9 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> |
| 10 <inputs> | 10 <inputs> |
| 11 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> | 11 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> |
| 12 </inputs> | 12 </inputs> |
| 24 </param> | 24 </param> |
| 25 <output type="data" format="RData" name="output" label="test-data/out.RData"/> | 25 <output type="data" format="RData" name="output" label="test-data/out.RData"/> |
| 26 </test> | 26 </test> |
| 27 </tests> | 27 </tests> |
| 28 <help> | 28 <help> |
| 29 **What it does** | 29 **What it does** |
| 30 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object | 30 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object |
| 31 **Input** | 31 **Input** |
| 32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" | 32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" |
| 33 **Output** | 33 **Output** |
| 34 GenomicRatioSet object | 34 GenomicRatioSet object |
| 35 </help> | 35 </help> |
| 36 <citations> | 36 <citations> |
| 37 <citation type="doi">10.1093/bioinformatics/btu049</citation> | 37 <citation type="doi">10.1093/bioinformatics/btu049</citation> |
| 38 </citations> | 38 </citations> |
| 39 </tool> | 39 </tool> |