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comparison bwa-mem2.xml @ 3:bfaa0d22c2e4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 689a4aeaf70a8e77be8589b1dcceb190f9df626a
author iuc
date Wed, 26 Jul 2023 20:02:13 +0000
parents b4a22d90cce9
children
comparison
equal deleted inserted replaced
2:b4a22d90cce9 3:bfaa0d22c2e4
69 ${analysis_type.io_options.V} 69 ${analysis_type.io_options.V}
70 ${analysis_type.io_options.Y} 70 ${analysis_type.io_options.Y}
71 ${analysis_type.io_options.M} 71 ${analysis_type.io_options.M}
72 ${analysis_type.io_options.five} 72 ${analysis_type.io_options.five}
73 ${analysis_type.io_options.q} 73 ${analysis_type.io_options.q}
74 #if str( $analysis_type.io_options.K ):
75 -K '${analysis_type.io_options.K}'
76 #end if
74 #end if 77 #end if
75 78
76 #end if 79 #end if
77 80
78 ## Handle read group options... 81 ## Handle read group options...
236 <!-- do nothing --> 239 <!-- do nothing -->
237 </when> 240 </when>
238 </conditional> 241 </conditional>
239 242
240 <conditional name="io_options"> 243 <conditional name="io_options">
241 <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options."> 244 <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, -M, and -K options.">
242 <option value="set">Set</option> 245 <option value="set">Set</option>
243 <option value="do_not_set" selected="True">Do not set</option> 246 <option value="do_not_set" selected="True">Do not set</option>
244 </param> 247 </param>
245 <when value="set"> 248 <when value="set">
246 <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"/> 249 <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"/>
250 <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"/> 253 <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"/>
251 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/> 254 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
252 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/> 255 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>
253 <param name="Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments" help="-Y; By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments" /> 256 <param name="Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments" help="-Y; By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments" />
254 <param name="M" type="boolean" truevalue="-M" falsevalue="" label="Mark shorter split hits of a chimeric alignment in the FLAG field as 'secondary alignment' instead of 'supplementary alignment'" help="-M; For Picard&lt;1.96 compatibility" /> 257 <param name="M" type="boolean" truevalue="-M" falsevalue="" label="Mark shorter split hits of a chimeric alignment in the FLAG field as 'secondary alignment' instead of 'supplementary alignment'" help="-M; For Picard&lt;1.96 compatibility" />
258 <param name="K" type="integer" optional="True" label="Process this number of input bases in each batch regardless of nThreads (for reproducibility)" help="-K"/>
255 </when> 259 </when>
256 <when value="do_not_set"> 260 <when value="do_not_set">
257 <!-- do nothing --> 261 <!-- do nothing -->
258 </when> 262 </when>
259 </conditional> 263 </conditional>