Mercurial > repos > testtool > get_gr_set
changeset 0:457c1fc71f64 draft
Uploaded
| author | testtool |
|---|---|
| date | Sun, 11 Jun 2017 06:21:37 -0400 |
| parents | |
| children | af176b97c4ac |
| files | getGRsetFromGEO/.Rapp.history getGRsetFromGEO/.Rhistory getGRsetFromGEO/._.DS_Store getGRsetFromGEO/getGRsetFromGEO.R getGRsetFromGEO/getGRsetFromGEO.xml getGRsetFromGEO/test-data/._.DS_Store getGRsetFromGEO/test-data/out.RData |
| diffstat | 6 files changed, 67 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGRsetFromGEO/.Rhistory Sun Jun 11 06:21:37 2017 -0400 @@ -0,0 +1,16 @@ +require("minfi", quietly = TRUE) +?require +require("minfi", quietly = TRUE) +minfi +as.data.frame(GRset) +GRset <- getGenomicRatioSetFromGEO(GSE) +getGenomicRatioSetFromGEO +require("minfi", quietly = TRUE) +options(warn = -1) +options("download.file.method"="wget") +args <- commandArgs(trailingOnly = TRUE) +GSE = args[1] +output = args[2] +GRset <- getGenomicRatioSetFromGEO(GSE) +save(GRset,file = output) +sessionInfo()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGRsetFromGEO/getGRsetFromGEO.R Sun Jun 11 06:21:37 2017 -0400 @@ -0,0 +1,12 @@ +require("minfi", quietly = TRUE) + +options(warn = -1) +options("download.file.method"="wget") + +args <- commandArgs(trailingOnly = TRUE) +GSE = args[1] +output = args[2] + +GRset <- getGenomicRatioSetFromGEO(GSE) + +save(GRset,file = output)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGRsetFromGEO/getGRsetFromGEO.xml Sun Jun 11 06:21:37 2017 -0400 @@ -0,0 +1,39 @@ +<?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>