Mercurial > repos > yhoogstrate > crossmap

changeset 37:9e99c09ebe84 draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
author yhoogstrate
date Thu, 12 Nov 2015 16:38:32 -0500
parents 47d4f148eb8c
children
files crossmap.xml test-data/bla.bam test-data/bla.sam
diffstat 3 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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>
Binary file test-data/bla.bam has changed
--- /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	*