# HG changeset patch
# User yhoogstrate
# Date 1447364312 18000
# Node ID 9e99c09ebe84c525d324ea8086c92ee153ecf29b
# Parent  47d4f148eb8cce29f5380806d0d2757c0386d1e3
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty

diff -r 47d4f148eb8c -r 9e99c09ebe84 crossmap.xml
--- a/crossmap.xml	Thu Nov 12 16:15:14 2015 -0500
+++ b/crossmap.xml	Thu Nov 12 16:38:32 2015 -0500
@@ -8,8 +8,9 @@
     </requirements>
     
     <stdio>
-        <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/>
+        <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
         <regex match=".*" source="both" level="log"/>
+        <exit_code range="1:" />
     </stdio>
     
     <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
diff -r 47d4f148eb8c -r 9e99c09ebe84 test-data/bla.bam
Binary file test-data/bla.bam has changed
diff -r 47d4f148eb8c -r 9e99c09ebe84 test-data/bla.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bla.sam	Thu Nov 12 16:38:32 2015 -0500
@@ -0,0 +1,3 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:1000051
+read_001	0	chr1	100000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*