Mercurial > repos > artbio > artbio_bam_cleaning

comparison artbio_bam_cleaning.xml @ 5:ebdaf5b3d6a7 draft

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"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
comparison
equal deleted inserted replaced
4:15ada8e1580a 5:ebdaf5b3d6a7
1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy4"> 1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy5">
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)' -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)' -f 'bam' $input_base".bam"
23 #if $skip_rmdup == 'no': 23 #if $skip_rmdup == 'no':
24 | samtools rmdup -s - - | tee $input_base".filt1.dedup.bam" 24 | samtools rmdup -s - - | tee $input_base".filt1.dedup.bam"
25 #end if 25 #end if
26 | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" - 26 | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
27 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $calmd 27 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
28 && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd 28 | tee $calmd
29 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
29 ]]></command> 30 ]]></command>
30 <inputs> 31 <inputs>
31 <expand macro="reference_source_conditional" /> 32 <expand macro="reference_source_conditional" />
32 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/> 33 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
33 <param name="skip_rmdup" type="select" label="skip remove pcr duplicate step ?" display="radio" 34 <param name="skip_rmdup" type="select" label="skip remove pcr duplicate step ?" display="radio"