# HG changeset patch
# User artbio
# Date 1641730538 0
# Node ID 6815060fb0561f57314371c212a105000041caa9
# Parent  ba3e6a71acb80efdc13fe0206d4f1f514d72b0a6
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 667afd5a5408321a31cdebab75b378e694deab07"

diff -r ba3e6a71acb8 -r 6815060fb056 artbio_bam_cleaning.xml
--- a/artbio_bam_cleaning.xml	Fri Dec 31 00:04:07 2021 +0000
+++ b/artbio_bam_cleaning.xml	Sun Jan 09 12:15:38 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy3">
+<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy4">
     <description>
         on flags and PCR Duplicates and MD recalibration
     </description>
@@ -26,9 +26,9 @@
         > $calmd
     #else if $specify_outputs == 'both':
         | tee $calmd
-        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
+        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254 and proper_pair' -f 'bam' /dev/stdin > $fullfilter
     #else:
-        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
+        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254 and proper_pair' -f 'bam' /dev/stdin > $fullfilter
     #end if
     ]]></command>
     <inputs>
@@ -40,7 +40,7 @@
                      aberrant Mapping Quality alignements generated by calMD recalibration.
                      One, the other, or both types of outputs can be retained by the tool">
             <option value="just_calMD">Alignments are only MD-recalibrated (for split or discordant read aware variant callers)</option>
-            <option value="calMDandMQ" selected="true">Alignments are MD-recalibrated AND mapping quality &gt; 254 are discarded (for snv and small indel callers)</option>
+            <option value="calMDandMQ" selected="true">Alignments are MD-recalibrated AND mapping quality &gt; 254 are discarded AND only proper_pair flag is retained (for snv and small indel callers)</option>
             <option value="both">Both types of outputs are retained</option>
         </param>
     </inputs>
diff -r ba3e6a71acb8 -r 6815060fb056 test-data/full.bam
Binary file test-data/full.bam has changed