Mercurial > repos > testtool > get_geo

changeset 36:a266a7c268e9 draft

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Uploaded
author testtool
date Thu, 09 Feb 2017 10:13:04 -0500
parents 0262f5edecb9
children ec7a1f7f9a94
files GEO/getGEO.R GEO/getGEO.xml
diffstat 2 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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]
--- 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">