Mercurial > repos > testtool > get_geo
changeset 32:2b223a449cf6 draft
Uploaded
| author | testtool |
|---|---|
| date | Thu, 09 Feb 2017 08:56:42 -0500 |
| parents | f81cbc34657c |
| children | 336f56093613 |
| files | GEO/.Rhistory GEO/getGEO.R GEO/getGEO.xml |
| diffstat | 3 files changed, 10 insertions(+), 4 deletions(-) [+] |
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--- a/GEO/.Rhistory Thu Feb 09 08:42:04 2017 -0500 +++ b/GEO/.Rhistory Thu Feb 09 08:56:42 2017 -0500 @@ -0,0 +1,5 @@ +??options +options(warn = -1) ++options("download.file.method"="wget") +options("download.file.method"="wget") +options(warn = -1,"download.file.method"="wget")
--- a/GEO/getGEO.R Thu Feb 09 08:42:04 2017 -0500 +++ b/GEO/getGEO.R Thu Feb 09 08:56:42 2017 -0500 @@ -4,7 +4,8 @@ require("rtracklayer", quietly = TRUE) require("FDb.InfiniumMethylation.hg19", quietly = TRUE) -options(warn = -1) +options(warn = -1,"download.file.method"="wget") + args <- commandArgs(trailingOnly = TRUE) GSMTable = args[1] MetaTable = args[2]
--- a/GEO/getGEO.xml Thu Feb 09 08:42:04 2017 -0500 +++ b/GEO/getGEO.xml Thu Feb 09 08:56:42 2017 -0500 @@ -3,9 +3,9 @@ <requirements> <requirement type="package" version="3.2.1">R</requirement> </requirements> -<stdio> -<exit_code range="1:"/> -</stdio> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command> <inputs> <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">