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comparison bwa-mem.xml @ 16:be4e38d127ae draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit e1191c87a0fccfafa0f23c3bd09f416a6700b387
author devteam
date Tue, 21 Nov 2017 09:11:39 -0500
parents 4d82cf59895e
children 48f306c57611
comparison
equal deleted inserted replaced
15:4d82cf59895e 16:be4e38d127ae
62 ${analysis_type.io_options.C} 62 ${analysis_type.io_options.C}
63 ${analysis_type.io_options.V} 63 ${analysis_type.io_options.V}
64 ${analysis_type.io_options.Y} 64 ${analysis_type.io_options.Y}
65 ${analysis_type.io_options.M} 65 ${analysis_type.io_options.M}
66 ${analysis_type.io_options.five} 66 ${analysis_type.io_options.five}
67 ${analysis_type.io_options.q}
67 #end if 68 #end if
68 69
69 #end if 70 #end if
70 71
71 ## Handle read group options... 72 ## Handle read group options...
226 <option value="set">Set</option> 227 <option value="set">Set</option>
227 <option value="do_not_set" selected="True">Do not set</option> 228 <option value="do_not_set" selected="True">Do not set</option>
228 </param> 229 </param>
229 <when value="set"> 230 <when value="set">
230 <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/> 231 <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/>
232 <param argument="-q" type="boolean" truevalue="-q" falsevalue="" label="Don't lower MAPQ for split alignment" help="By default the MAPQ score of a supplementary alignment will be lowered to the primary alignment score."/>
231 <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/> 233 <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
232 <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" /> 234 <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" />
233 <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/> 235 <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>
234 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/> 236 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
235 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/> 237 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>