Mercurial > repos > devteam > bwa
comparison bwa-mem.xml @ 15:4d82cf59895e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit dead2eaab58698fe02b8bb068f8d859eba551e8d
author | devteam |
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date | Sat, 30 Sep 2017 13:37:06 -0400 |
parents | 051eba708f43 |
children | be4e38d127ae |
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14:051eba708f43 | 15:4d82cf59895e |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2"> | 2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.0"> |
3 <description>- map medium and long reads (> 100 bp) against reference genome</description> | 3 <description>- map medium and long reads (> 100 bp) against reference genome</description> |
4 <macros> | 4 <macros> |
5 <import>read_group_macros.xml</import> | 5 <import>read_group_macros.xml</import> |
6 <import>bwa_macros.xml</import> | 6 <import>bwa_macros.xml</import> |
7 </macros> | 7 </macros> |
61 ${analysis_type.io_options.a} | 61 ${analysis_type.io_options.a} |
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 #end if | 67 #end if |
67 | 68 |
68 #end if | 69 #end if |
69 | 70 |
70 ## Handle read group options... | 71 ## Handle read group options... |
224 <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options."> | 225 <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options."> |
225 <option value="set">Set</option> | 226 <option value="set">Set</option> |
226 <option value="do_not_set" selected="True">Do not set</option> | 227 <option value="do_not_set" selected="True">Do not set</option> |
227 </param> | 228 </param> |
228 <when value="set"> | 229 <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"/> | |
229 <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/> | 231 <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/> |
230 <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score >80% of the max score, output them all in the XA tag" help="-h; default=5" /> | 232 <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score >80% of the max score, output them all in the XA tag" help="-h; default=5" /> |
231 <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"/> | 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"/> |
232 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/> | 234 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/> |
233 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/> | 235 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/> |