Mercurial > repos > artbio > artbio_bam_cleaning

comparison artbio_bam_cleaning.xml @ 3:a1462dd52f17 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b022da54be013bf593ad96de6e7bd8b9e6bb5523"
author artbio
date Tue, 16 Feb 2021 00:19:57 +0000
parents c973ff00c785
children 15ada8e1580a
comparison
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2:c973ff00c785 3:a1462dd52f17
1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy2"> 1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+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>
21 ln -s $input_bam input.bam && 21 ln -s $input_bam input.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" 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 > $calmd 25 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $calmd
26 #if $pipeline == 'fullfilter':
27 && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd 26 && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd
28 #end if
29 ]]></command> 27 ]]></command>
30 <inputs> 28 <inputs>
31 <expand macro="reference_source_conditional" /> 29 <expand macro="reference_source_conditional" />
32 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/> 30 <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>
37 </inputs> 31 </inputs>
38 <outputs> 32 <outputs>
39 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)"> 33 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" />
40 <filter>pipeline == 'CalMD'</filter> 34 <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" />
41 </data>
42 <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
43 <filter>pipeline == 'fullfilter'</filter>
44 </data>
45
46 </outputs> 35 </outputs>
47 <tests> 36 <tests>
48 <test> 37 <test>
49 <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" /> 38 <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
50 <param name="reference_source_selector" value="history" /> 39 <param name="reference_source_selector" value="history" />
51 <param name="ref_file" value="chr21.fa" /> 40 <param name="ref_file" value="chr21.fa" />
41 <output name="calmd" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam" ftype="bam" />
52 <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" /> 42 <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"/>
59 <output name="calmd" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam" ftype="bam" />
60 </test> 43 </test>
61 </tests> 44 </tests>
62 <help> 45 <help>
63 ARTbio bam cleaning overview 46 ARTbio bam cleaning overview
64 ============================ 47 ============================