# HG changeset patch
# User iuc
# Date 1466002224 14400
# Node ID bd79c4d39af0befc3087ee85a46907083c8dd406
# Parent  ebbf2a6a4c553906b0f3b7a85941211aacc0d3b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3

diff -r ebbf2a6a4c55 -r bd79c4d39af0 bam_to_scidx.xml
--- a/bam_to_scidx.xml	Tue Apr 19 18:10:09 2016 -0400
+++ b/bam_to_scidx.xml	Wed Jun 15 10:50:24 2016 -0400
@@ -3,6 +3,14 @@
     <requirements>
         <requirement type="package" version="8.0.45">java-jdk</requirement>
     </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range=":-1" />
+        <exit_code range="1:" />
+        <!-- Check stderr in case the return code has not been set -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
     <command>
         <![CDATA[
             ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" &&