Mercurial > repos > artbio > artbio_bam_cleaning

comparison artbio_bam_cleaning.xml @ 1:b550841f568b draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 2d441fd84bf17c0899d0b57ea35c84cb83b77119"
author artbio
date Thu, 08 Oct 2020 14:55:04 +0000
parents 65d6d2b554b3
children c973ff00c785
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0:65d6d2b554b3 1:b550841f568b
1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy0"> 1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy1">
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>
17 @pipefail@ 17 @pipefail@
18 @set_fasta_index@ 18 @set_fasta_index@
19 #set input_base = 'input' 19 #set input_base = 'input'
20 ln -f -s $input_bam.metadata.bam_index input.bam.bai && 20 ln -f -s $input_bam.metadata.bam_index input.bam.bai &&
21 ln -s $input_bam input.bam && 21 ln -s $input_bam input.bam &&
22 sambamba view -h -t 8 --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 | samtools rmdup - - 23 | samtools rmdup - -
24 |tee $input_base".filt1.dedup.bam"| bamleftalign --fasta-reference reference.fa -c --max-iterations "5" - 24 |tee $input_base".filt1.dedup.bam"| bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
25 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $input_base".filt1.dedup.bamleft.calmd.bam" && 25 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $calmd
26 sambamba view -h -t 8 --filter='mapping_quality <= 254' -f 'bam' -o $input_base".filt1.dedup.bamleft.calmd.filt2.bam" $input_base".filt1.dedup.bamleft.calmd.bam" 26 #if $pipeline == 'fullfilter':
27 && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd
28 #end if
27 ]]></command> 29 ]]></command>
28 <inputs> 30 <inputs>
29 <expand macro="reference_source_conditional" /> 31 <expand macro="reference_source_conditional" />
30 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/> 32 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
33 <param name="pipeline" type="select" label="where to stop the pipeline">
34 <option value="CalMD">At CalMD processing, to keep split read alignments</option>
35 <option value="fullfilter" selected="true">Full bam processing, will eliminate split read alignments in the final bam file</option>
36 </param>
31 </inputs> 37 </inputs>
32 <outputs> 38 <outputs>
33 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" from_work_dir="./input.filt1.dedup.bamleft.calmd.bam"/> 39 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)">
34 <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" from_work_dir="./input.filt1.dedup.bamleft.calmd.filt2.bam"/> 40 <filter>pipeline == 'CalMD'</filter>
41 </data>
42 <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
43 <filter>pipeline == 'fullfilter'</filter>
44 </data>
45
35 </outputs> 46 </outputs>
36 <tests> 47 <tests>
37 <test> 48 <test>
38 <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" /> 49 <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
39 <param name="reference_source_selector" value="history" /> 50 <param name="reference_source_selector" value="history" />
40 <param name="ref_file" value="chr21.fa" /> 51 <param name="ref_file" value="chr21.fa" />
52 <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" />
53 </test>
54 <test>
55 <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
56 <param name="reference_source_selector" value="history" />
57 <param name="ref_file" value="chr21.fa" />
58 <param name="pipeline" value="CalMD"/>
41 <output name="calmd" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam" ftype="bam" /> 59 <output name="calmd" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam" ftype="bam" />
42 <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" />
43 </test> 60 </test>
44 </tests> 61 </tests>
45 <help> 62 <help>
46 ARTbio bam cleaning overview 63 ARTbio bam cleaning overview
47 ============================ 64 ============================