Mercurial > repos > artbio > artbio_bam_cleaning
changeset 4:15ada8e1580a draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 13e2d0837000c2557f9590aa861a9fd5bc16cbcc"
| author | artbio |
|---|---|
| date | Tue, 16 Mar 2021 23:38:46 +0000 |
| parents | a1462dd52f17 |
| children | ebdaf5b3d6a7 |
| files | artbio_bam_cleaning.xml test-data/calmd.bam test-data/full.bam test-data/match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam test-data/match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam test-data/normdup_calmd.bam test-data/normdup_full.bam |
| diffstat | 7 files changed, 20 insertions(+), 5 deletions(-) [+] |
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--- a/artbio_bam_cleaning.xml Tue Feb 16 00:19:57 2021 +0000 +++ b/artbio_bam_cleaning.xml Tue Mar 16 23:38:46 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy3"> +<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy4"> <description> on flags and PCR Duplicates and MD recalibration </description> @@ -20,14 +20,21 @@ ln -f -s $input_bam.metadata.bam_index input.bam.bai && ln -s $input_bam input.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" - + #if $skip_rmdup == 'no': + | samtools rmdup -s - - | tee $input_base".filt1.dedup.bam" + #end if + | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" - | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $calmd && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd ]]></command> <inputs> <expand macro="reference_source_conditional" /> <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/> + <param name="skip_rmdup" type="select" label="skip remove pcr duplicate step ?" display="radio" + help="useful if duplicates are already marked by other tools"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> </inputs> <outputs> <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" /> @@ -38,8 +45,16 @@ <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="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" /> + <output name="calmd" file="calmd.bam" ftype="bam" /> + <output name="fullfilter" file="full.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="skip_rmdup" value="yes" /> + <param name="ref_file" value="chr21.fa" /> + <output name="calmd" file="normdup_calmd.bam" ftype="bam" /> + <output name="fullfilter" file="normdup_full.bam" ftype="bam" /> </test> </tests> <help>