Mercurial > repos > artbio > artbio_bam_cleaning
diff artbio_bam_cleaning.xml @ 5:ebdaf5b3d6a7 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b846085c8b8e29bb067a3cdcb90355117aeebf42"
| author | artbio |
|---|---|
| date | Mon, 29 Mar 2021 15:09:23 +0000 |
| parents | 15ada8e1580a |
| children | 999c2b871f36 |
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--- a/artbio_bam_cleaning.xml Tue Mar 16 23:38:46 2021 +0000 +++ b/artbio_bam_cleaning.xml Mon Mar 29 15:09:23 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy4"> +<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy5"> <description> on flags and PCR Duplicates and MD recalibration </description> @@ -24,8 +24,9 @@ | samtools rmdup -s - - | tee $input_base".filt1.dedup.bam" #end if | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" - - | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $calmd - && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd + | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa + | tee $calmd + | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter ]]></command> <inputs> <expand macro="reference_source_conditional" />