Mercurial > repos > artbio > artbio_bam_cleaning
changeset 1:b550841f568b draft
"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 |
| files | artbio_bam_cleaning.xml |
| diffstat | 1 files changed, 24 insertions(+), 7 deletions(-) [+] |
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--- a/artbio_bam_cleaning.xml Fri Oct 02 00:17:33 2020 +0000 +++ b/artbio_bam_cleaning.xml Thu Oct 08 14:55:04 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy0"> +<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy1"> <description> on flags and PCR Duplicates and MD recalibration </description> @@ -19,27 +19,44 @@ #set input_base = 'input' ln -f -s $input_bam.metadata.bam_index input.bam.bai && ln -s $input_bam input.bam && - sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input_base".bam" + sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input_base".bam" | samtools rmdup - - |tee $input_base".filt1.dedup.bam"| bamleftalign --fasta-reference reference.fa -c --max-iterations "5" - - | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $input_base".filt1.dedup.bamleft.calmd.bam" && - 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" + | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $calmd + #if $pipeline == 'fullfilter': + && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd + #end if ]]></command> <inputs> <expand macro="reference_source_conditional" /> <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/> + <param name="pipeline" type="select" label="where to stop the pipeline"> + <option value="CalMD">At CalMD processing, to keep split read alignments</option> + <option value="fullfilter" selected="true">Full bam processing, will eliminate split read alignments in the final bam file</option> + </param> </inputs> <outputs> - <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" from_work_dir="./input.filt1.dedup.bamleft.calmd.bam"/> - <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" from_work_dir="./input.filt1.dedup.bamleft.calmd.filt2.bam"/> + <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)"> + <filter>pipeline == 'CalMD'</filter> + </data> + <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)"> + <filter>pipeline == 'fullfilter'</filter> + </data> + </outputs> <tests> <test> <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" /> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="chr21.fa" /> + <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" /> + </test> + <test> + <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="chr21.fa" /> + <param name="pipeline" value="CalMD"/> <output name="calmd" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam" ftype="bam" /> - <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" /> </test> </tests> <help>