Mercurial > repos > artbio > artbio_bam_cleaning

comparison artbio_bam_cleaning.xml @ 6:999c2b871f36 draft

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"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
comparison
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5:ebdaf5b3d6a7 6:999c2b871f36
1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy5"> 1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy6">
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>
23 #if $skip_rmdup == 'no': 23 #if $skip_rmdup == 'no':
24 | samtools rmdup -s - - | tee $input_base".filt1.dedup.bam" 24 | samtools rmdup -s - - | tee $input_base".filt1.dedup.bam"
25 #end if 25 #end if
26 | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" - 26 | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
27 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa 27 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
28 | tee $calmd 28 #if $skip_laststep == 'yes':
29 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter 29 > $calmd
30 #else if $skip_laststep == 'no':
31 | tee $calmd
32 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
33 #end if
30 ]]></command> 34 ]]></command>
31 <inputs> 35 <inputs>
32 <expand macro="reference_source_conditional" /> 36 <expand macro="reference_source_conditional" />
33 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/> 37 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
34 <param name="skip_rmdup" type="select" label="skip remove pcr duplicate step ?" display="radio" 38 <param name="skip_rmdup" type="select" label="skip remove pcr duplicate step ?" display="radio"
35 help="useful if duplicates are already marked by other tools"> 39 help="useful if duplicates are already marked by other tools">
36 <option value="no" selected="true">No</option> 40 <option value="no" selected="true">No</option>
37 <option value="yes">Yes</option> 41 <option value="yes">Yes</option>
38 </param> 42 </param>
43 <param name="skip_laststep" type="select" label="skip last samtool view filter ?" display="radio"
44 help="Only generate the calMD output">
45 <option value="no" selected="true">No</option>
46 <option value="yes">Yes</option>
47 </param>
39 </inputs> 48 </inputs>
40 <outputs> 49 <outputs>
41 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" /> 50 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" />
42 <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" /> 51 <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
52 <filter>skip_laststep == "no"</filter>
53 </data>
43 </outputs> 54 </outputs>
44 <tests> 55 <tests>
45 <test> 56 <test>
46 <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" /> 57 <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
47 <param name="reference_source_selector" value="history" /> 58 <param name="reference_source_selector" value="history" />