Mercurial > repos > testtool > get_gr_set
changeset 1:af176b97c4ac draft
Deleted selected files
| author | testtool |
|---|---|
| date | Sun, 11 Jun 2017 06:37:18 -0400 |
| parents | 457c1fc71f64 |
| children | 39f1afe94ef4 |
| files | getGRsetFromGEO/getGRsetFromGEO.xml |
| diffstat | 1 files changed, 0 insertions(+), 39 deletions(-) [+] |
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--- a/getGRsetFromGEO/getGRsetFromGEO.xml Sun Jun 11 06:21:37 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="getGRsetFromGEO" name="getGRsetFromGEO" version="1.18.4"> - <requirements> - <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> - </requirements> -<stdio> - <exit_code range="1:" /> -</stdio> - <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> - <inputs> - <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> - </inputs> - <outputs> - <data format="RDdata" name="output" label="GRsetFromGEO.RData"/> - </outputs> - <tests> - <test> - <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSE" value="GSE51547"/> - </collection> - </element> - </param> - <output type="data" format="RData" name="output" label="test-data/out.RData"/> - </test> - </tests> - <help> -**What it does** -This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object -**Input** -The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" -**Output** -GenomicRatioSet object -</help> -<citations> -<citation type="doi">10.1093/bioinformatics/btu049</citation> -</citations> -</tool>