# HG changeset patch
# User artbio
# Date 1640906644 0
# Node ID cb94e94e0f4e00fa391e0cffa767b809af524bad
# Parent  b12e50bcddd252480cd4373205b1b4467331e89a
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit ed02ebb9addd947f34d9491420bc325e941eb468"

diff -r b12e50bcddd2 -r cb94e94e0f4e artbio_bam_cleaning.xml
--- a/artbio_bam_cleaning.xml	Thu Dec 30 19:53:07 2021 +0000
+++ b/artbio_bam_cleaning.xml	Thu Dec 30 23:24:04 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy1">
+<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy2">
     <description>
         on flags and PCR Duplicates and MD recalibration
     </description>
@@ -27,6 +27,8 @@
     #else if $specify_outputs == 'calMDandMQ' or $specify_outputs == 'both':
         | tee $calmd
         | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
+    #else:
+        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
     #end if
     ]]></command>
     <inputs>