# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1370861033 18000
# Node ID d975e466d4435aec9b13106a81f510c610fc2935
# Parent  85693cb5339fa1278b629d72d8c58470987ea316
Add stdio tag to create_reference_dataset.xml

diff -r 85693cb5339f -r d975e466d443 create_reference_dataset.xml
--- a/create_reference_dataset.xml	Sun Jun 09 21:21:03 2013 -0500
+++ b/create_reference_dataset.xml	Mon Jun 10 05:43:53 2013 -0500
@@ -9,7 +9,7 @@
  </requirements>
   <command interpreter="command"> /bin/bash $shscript </command>
  <inputs>
-  <param name="ensembl_genome_version" type="text" value="" label="Esembl Genome Version" help="Example: GRCh37"/>
+  <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Example: GRCh37"/>
   <param name="ensembl_version" type="integer" value="" label="Esembl Release Version" help="Example: 71"/>
   <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Example: hg19"/>
   <param name="chromosomes" type="text" value="" label="Chromosomes" help="Example: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
@@ -21,6 +21,14 @@
  <outputs>
   <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
  </outputs>
+  <stdio>
+    <exit_code range="1:"  level="fatal"   description="Error running Create DeFuse Reference" />
+    <regex match="Error:" 
+           source="both" 
+           level="fatal" 
+           description="Error running Create DeFuse Reference" />
+
+  </stdio>
  <configfiles>
   <configfile name="defuse_config">
 #import ast