Mercurial > repos > testtool > get_geo

changeset 32:2b223a449cf6 draft

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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(-) [+]
line wrap: on
line diff
--- 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">