Mercurial > repos > artbio > artbio_bam_cleaning
changeset 11:6815060fb056 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 667afd5a5408321a31cdebab75b378e694deab07"
| author | artbio |
|---|---|
| date | Sun, 09 Jan 2022 12:15:38 +0000 |
| parents | ba3e6a71acb8 |
| children | b0f65f88411f |
| files | artbio_bam_cleaning.xml test-data/full.bam |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- 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 > 254 are discarded (for snv and small indel callers)</option> + <option value="calMDandMQ" selected="true">Alignments are MD-recalibrated AND mapping quality > 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>