Mercurial > repos > artbio > artbio_bam_cleaning
changeset 10:ba3e6a71acb8 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 4a36bccf4c745cc7f1f13189140252721ff5e61d"
| author | artbio |
|---|---|
| date | Fri, 31 Dec 2021 00:04:07 +0000 |
| parents | cb94e94e0f4e |
| children | 6815060fb056 |
| files | artbio_bam_cleaning.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- 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: