Mercurial > repos > artbio > artbio_bam_cleaning

comparison artbio_bam_cleaning.xml @ 2:c973ff00c785 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit c761c76bb178d141766850b2b35de4c70a844231"
author artbio
date Sun, 14 Feb 2021 22:45:31 +0000
parents b550841f568b
children a1462dd52f17
comparison
equal deleted inserted replaced
1:b550841f568b 2:c973ff00c785
1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy1"> 1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy2">
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>
29 ]]></command> 29 ]]></command>
30 <inputs> 30 <inputs>
31 <expand macro="reference_source_conditional" /> 31 <expand macro="reference_source_conditional" />
32 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/> 32 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
33 <param name="pipeline" type="select" label="where to stop the pipeline"> 33 <param name="pipeline" type="select" label="where to stop the pipeline">
34 <option value="CalMD">At CalMD processing, to keep split read alignments</option> 34 <option value="CalMD">At CalMD processing to keep split read alignments</option>
35 <option value="fullfilter" selected="true">Full bam processing, will eliminate split read alignments in the final bam file</option> 35 <option value="fullfilter" selected="true">Full bam processing, will eliminate split read alignments in the final bam file</option>
36 </param> 36 </param>
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)"> 39 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)">