Mercurial > repos > artbio > artbio_bam_cleaning
diff artbio_bam_cleaning.xml @ 3:a1462dd52f17 draft
"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 |
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--- a/artbio_bam_cleaning.xml Sun Feb 14 22:45:31 2021 +0000 +++ b/artbio_bam_cleaning.xml Tue Feb 16 00:19:57 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy2"> +<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy3"> <description> on flags and PCR Duplicates and MD recalibration </description> @@ -23,41 +23,24 @@ | 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 > $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)"> - <filter>pipeline == 'CalMD'</filter> - </data> - <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)"> - <filter>pipeline == 'fullfilter'</filter> - </data> - + <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" /> + <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" /> </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="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> - <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" /> - </test> </tests> <help> ARTbio bam cleaning overview