# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1347646322 18000
# Node ID c641d515de2ec559ea7adf5618466e7efdb6631d
# Parent  ceaa79a5ee166a193e01fab50c382e6d4a8cd1ff
Add stdio tags

diff -r ceaa79a5ee16 -r c641d515de2e snpEff.xml
--- a/snpEff.xml	Fri Sep 14 07:51:23 2012 -0500
+++ b/snpEff.xml	Fri Sep 14 13:12:02 2012 -0500
@@ -481,7 +481,10 @@
 		</data>
 		<data format="html" name="statsFile" />
 	</outputs>
-
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
 	<help>
 
 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
diff -r ceaa79a5ee16 -r c641d515de2e snpEff_download.xml
--- a/snpEff_download.xml	Fri Sep 14 07:51:23 2012 -0500
+++ b/snpEff_download.xml	Fri Sep 14 13:12:02 2012 -0500
@@ -413,6 +413,10 @@
 	<outputs>
 		<data format="txt" name="logfile" />
 	</outputs>
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
 
 	<help>
 
diff -r ceaa79a5ee16 -r c641d515de2e snpSift_annotate.xml
--- a/snpSift_annotate.xml	Fri Sep 14 07:51:23 2012 -0500
+++ b/snpSift_annotate.xml	Fri Sep 14 13:12:02 2012 -0500
@@ -14,7 +14,8 @@
 		<param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
 	</inputs>
         <stdio>
-          <exit_code range="-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
         </stdio>
 
 	<outputs>
diff -r ceaa79a5ee16 -r c641d515de2e snpSift_caseControl.xml
--- a/snpSift_caseControl.xml	Fri Sep 14 07:51:23 2012 -0500
+++ b/snpSift_caseControl.xml	Fri Sep 14 13:12:02 2012 -0500
@@ -28,6 +28,10 @@
 	<outputs>
 		<data format="vcf" name="output" />
 	</outputs>
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
 
 	<help>
 
diff -r ceaa79a5ee16 -r c641d515de2e snpSift_filter.xml
--- a/snpSift_filter.xml	Fri Sep 14 07:51:23 2012 -0500
+++ b/snpSift_filter.xml	Fri Sep 14 13:12:02 2012 -0500
@@ -26,7 +26,10 @@
 	<outputs>
 		<data format="vcf" name="output" />
 	</outputs>
-
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
 	<help>
 
 You can filter using arbitrary expressions.
diff -r ceaa79a5ee16 -r c641d515de2e snpSift_int.xml
--- a/snpSift_int.xml	Fri Sep 14 07:51:23 2012 -0500
+++ b/snpSift_int.xml	Fri Sep 14 13:12:02 2012 -0500
@@ -18,7 +18,10 @@
 	<outputs>
 		<data format="vcf" name="output" />
 	</outputs>
-
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
 	<help>
 
 You can filter using intervals (BED file)