Mercurial > repos > artbio > artbio_bam_cleaning

changeset 9:cb94e94e0f4e draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit ed02ebb9addd947f34d9491420bc325e941eb468"
author artbio
date Thu, 30 Dec 2021 23:24:04 +0000
parents b12e50bcddd2
children ba3e6a71acb8
files artbio_bam_cleaning.xml
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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>