Mercurial > repos > iuc > bbtools_bbmap

comparison bbmap.xml @ 13:456d8ebb6a28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:15:02 +0000
parents 3f94a2e3d513
children 8015d7ab8357
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12:3f94a2e3d513 13:456d8ebb6a28
200 <option value="lr">Trim both</option> 200 <option value="lr">Trim both</option>
201 </param> 201 </param>
202 <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/> 202 <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/>
203 <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/> 203 <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
204 <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/> 204 <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
205 <param argument="fakefastaquality" type="integer" value="-1" max="50" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/> 205 <param argument="fakefastaquality" type="integer" max="50" value="-1" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
206 <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/> 206 <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/>
207 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/> 207 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
208 <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/> 208 <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/>
209 <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/> 209 <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/>
210 </section> 210 </section>
223 <option value="name">Sort by read names</option> 223 <option value="name">Sort by read names</option>
224 <option value="unsorted">Not sorted (sorted as input)</option> 224 <option value="unsorted">Not sorted (sorted as input)</option>
225 </param> 225 </param>
226 </section> 226 </section>
227 <section name="pf_options" title="Post-filtering options"> 227 <section name="pf_options" title="Post-filtering options">
228 <param argument="idfilter" type="integer" value="0" min="0" max="1" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/> 228 <param argument="idfilter" type="integer" min="0" max="1" value="0" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
229 <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/> 229 <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/>
230 <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/> 230 <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/>
231 <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/> 231 <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/>
232 <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/> 232 <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/>
233 <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/> 233 <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/>
363 * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file. 363 * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file.
364 364
365 </help> 365 </help>
366 <expand macro="citations"/> 366 <expand macro="citations"/>
367 </tool> 367 </tool>
368