# HG changeset patch
# User artbio
# Date 1640909047 0
# Node ID ba3e6a71acb80efdc13fe0206d4f1f514d72b0a6
# Parent  cb94e94e0f4e00fa391e0cffa767b809af524bad
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 4a36bccf4c745cc7f1f13189140252721ff5e61d"

diff -r cb94e94e0f4e -r ba3e6a71acb8 artbio_bam_cleaning.xml
--- a/artbio_bam_cleaning.xml	Thu Dec 30 23:24:04 2021 +0000
+++ b/artbio_bam_cleaning.xml	Fri Dec 31 00:04:07 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy2">
+<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy3">
     <description>
         on flags and PCR Duplicates and MD recalibration
     </description>
@@ -24,7 +24,7 @@
     | samtools calmd  -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
     #if $specify_outputs == 'just_calMD':
         > $calmd
-    #else if $specify_outputs == 'calMDandMQ' or $specify_outputs == 'both':
+    #else if $specify_outputs == 'both':
         | tee $calmd
         | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
     #else: