Mercurial > repos > artbio > artbio_bam_cleaning

comparison artbio_bam_cleaning.xml @ 10:ba3e6a71acb8 draft

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"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
comparison
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9:cb94e94e0f4e 10:ba3e6a71acb8
1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy2"> 1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy3">
2 <description> 2 <description>
3 on flags and PCR Duplicates and MD recalibration 3 on flags and PCR Duplicates and MD recalibration
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macro.xml</import> 6 <import>macro.xml</import>
22 sambamba view -h -t \${GALAXY_SLOTS:-2} --filter="mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped) and not(duplicate)" -f "bam" ${input_base}".bam" 22 sambamba view -h -t \${GALAXY_SLOTS:-2} --filter="mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped) and not(duplicate)" -f "bam" ${input_base}".bam"
23 | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" - 23 | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
24 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa 24 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
25 #if $specify_outputs == 'just_calMD': 25 #if $specify_outputs == 'just_calMD':
26 > $calmd 26 > $calmd
27 #else if $specify_outputs == 'calMDandMQ' or $specify_outputs == 'both': 27 #else if $specify_outputs == 'both':
28 | tee $calmd 28 | tee $calmd
29 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter 29 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
30 #else: 30 #else:
31 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter 31 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
32 #end if 32 #end if