# HG changeset patch
# User sblanck
# Date 1491983042 14400
# Node ID b01c4f2600855aa5c5fffc803fa47bb4afc5814e
# Parent  93451f832736a6bf51fc4762b11bb852ff24c943
use optparse

diff -r 93451f832736 -r b01c4f260085 GEOQuery.xml
--- a/GEOQuery.xml	Tue Mar 21 10:28:47 2017 -0400
+++ b/GEOQuery.xml	Wed Apr 12 03:44:02 2017 -0400
@@ -1,18 +1,21 @@
 <tool id="GEOQuery" name="GEOQuery">
 	<description>GEOQuery wrapper</description>
+	<stdio>
+        <exit_code range="1:" />
+    </stdio>
 	<requirements>
 	  	<!--container type="docker">sblanck/smagexp</container-->
 		<requirement type="package" version="0.1.0">r-smagexp</requirement>
 	</requirements>
-	<command interpreter="python">
+	<command>
 		<![CDATA[ 
-			stderr_wrapper.py Rscript 
+			Rscript --vanilla
 			${__tool_directory__}/GEOQuery.R 
-			$GEOQueryID 
-			$GEOQueryData 
-			$GEOQueryRData 
-			$conditions
-			$transformation
+			--id ${GEOQueryID} 
+			--transformation ${transformation}
+			--data ${GEOQueryData} 
+			--rdata ${GEOQueryRData} 
+			--conditions ${conditions}
 		]]>
 	</command>
 
@@ -46,7 +49,6 @@
 **Example** of .cond file      	
 ::
 
- Sample ID 	Condition			Description
  GSM80460	series of 16 tumors	GSM80460 OSCE-2T SERIES OF 16 TUMORS
  GSM80461	series of 16 tumors	GSM80461 OSCE-4T Series of 16 Tumors
  GSM80462	series of 16 tumors	GSM80462 OSCE-6T Series of 16 Tumors