Mercurial > repos > artbio > artbio_bam_cleaning

comparison artbio_bam_cleaning.xml @ 11:6815060fb056 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 667afd5a5408321a31cdebab75b378e694deab07"
author artbio
date Sun, 09 Jan 2022 12:15:38 +0000
parents ba3e6a71acb8
children b0f65f88411f
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10:ba3e6a71acb8 11:6815060fb056
1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy3"> 1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy4">
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>
24 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa 24 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
25 #if $specify_outputs == 'just_calMD': 25 #if $specify_outputs == 'just_calMD':
26 > $calmd 26 > $calmd
27 #else if $specify_outputs == 'both': 27 #else if $specify_outputs == 'both':
28 | tee $calmd 28 | tee $calmd
29 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter 29 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254 and proper_pair' -f 'bam' /dev/stdin > $fullfilter
30 #else: 30 #else:
31 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter 31 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254 and proper_pair' -f 'bam' /dev/stdin > $fullfilter
32 #end if 32 #end if
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <expand macro="reference_source_conditional" /> 35 <expand macro="reference_source_conditional" />
36 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/> 36 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
38 display="radio" 38 display="radio"
39 help="The tool first generates MD-recalibrated alignements, then discards 39 help="The tool first generates MD-recalibrated alignements, then discards
40 aberrant Mapping Quality alignements generated by calMD recalibration. 40 aberrant Mapping Quality alignements generated by calMD recalibration.
41 One, the other, or both types of outputs can be retained by the tool"> 41 One, the other, or both types of outputs can be retained by the tool">
42 <option value="just_calMD">Alignments are only MD-recalibrated (for split or discordant read aware variant callers)</option> 42 <option value="just_calMD">Alignments are only MD-recalibrated (for split or discordant read aware variant callers)</option>
43 <option value="calMDandMQ" selected="true">Alignments are MD-recalibrated AND mapping quality &gt; 254 are discarded (for snv and small indel callers)</option> 43 <option value="calMDandMQ" selected="true">Alignments are MD-recalibrated AND mapping quality &gt; 254 are discarded AND only proper_pair flag is retained (for snv and small indel callers)</option>
44 <option value="both">Both types of outputs are retained</option> 44 <option value="both">Both types of outputs are retained</option>
45 </param> 45 </param>
46 </inputs> 46 </inputs>
47 <outputs> 47 <outputs>
48 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)"> 48 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)">