Mercurial > repos > artbio > artbio_bam_cleaning
changeset 6:999c2b871f36 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
| author | artbio |
|---|---|
| date | Wed, 07 Apr 2021 01:31:51 +0000 |
| parents | ebdaf5b3d6a7 |
| children | 745f529127b8 |
| files | artbio_bam_cleaning.xml |
| diffstat | 1 files changed, 20 insertions(+), 9 deletions(-) [+] |
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--- a/artbio_bam_cleaning.xml Mon Mar 29 15:09:23 2021 +0000 +++ b/artbio_bam_cleaning.xml Wed Apr 07 01:31:51 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy5"> +<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy6"> <description> on flags and PCR Duplicates and MD recalibration </description> @@ -25,21 +25,32 @@ #end if | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" - | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa - | tee $calmd - | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter + #if $skip_laststep == 'yes': + > $calmd + #else if $skip_laststep == 'no': + | tee $calmd + | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter + #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="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> + <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> + <param name="skip_laststep" type="select" label="skip last samtool view filter ?" display="radio" + help="Only generate the calMD output"> + <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)" /> - <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" /> + <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)"> + <filter>skip_laststep == "no"</filter> + </data> </outputs> <tests> <test>