# HG changeset patch # User testtool # Date 1486653184 18000 # Node ID a266a7c268e98ca38e213e80582c2466cf19785c # Parent 0262f5edecb93b7c5d52fed10f5bb4dbb3e13f2c Uploaded diff -r 0262f5edecb9 -r a266a7c268e9 GEO/getGEO.R --- a/GEO/getGEO.R Thu Feb 09 09:56:43 2017 -0500 +++ b/GEO/getGEO.R Thu Feb 09 10:13:04 2017 -0500 @@ -4,7 +4,7 @@ require("rtracklayer", quietly = TRUE) require("FDb.InfiniumMethylation.hg19", quietly = TRUE) -options(warn = -1,"download.file.method"="wget") +options("download.file.method"="wget") args <- commandArgs(trailingOnly = TRUE) GSMTable = args[1] diff -r 0262f5edecb9 -r a266a7c268e9 GEO/getGEO.xml --- a/GEO/getGEO.xml Thu Feb 09 09:56:43 2017 -0500 +++ b/GEO/getGEO.xml Thu Feb 09 10:13:04 2017 -0500 @@ -3,6 +3,9 @@ <requirements> <requirement type="package" version="3.2.1">R</requirement> </requirements> + <stdio> + <exit_code range="1:"></exit_code> + </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">