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comparison bowtie2_wrapper.xml @ 34:cebb672ec7c1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 commit 805616637ccfe14dafcffddce7935d36d8243cc1
author iuc
date Thu, 05 Mar 2026 21:19:43 +0000
parents c3d19e7ee879
children
comparison
equal deleted inserted replaced
33:c3d19e7ee879 34:cebb672ec7c1
226 #end if 226 #end if
227 227
228 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes": 228 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
229 -D ${analysis_type.effort_options.D} 229 -D ${analysis_type.effort_options.D}
230 -R ${analysis_type.effort_options.R} 230 -R ${analysis_type.effort_options.R}
231 ${analysis_type.effort_options.d}
231 #end if 232 #end if
232 #if str( $analysis_type.other_options.other_options_selector ) == "yes": 233 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
233 ${analysis_type.other_options.non_deterministic} 234 ${analysis_type.other_options.non_deterministic}
234 --seed ${analysis_type.other_options.seed} 235 --seed ${analysis_type.other_options.seed}
235 #end if 236 #end if
420 <option value="no" selected="true">No</option> 421 <option value="no" selected="true">No</option>
421 </param> 422 </param>
422 <when value="yes"> 423 <when value="yes">
423 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/> 424 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/>
424 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/> 425 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/>
426 <param argument="-d" type="boolean" truevalue="-d" falsevalue="" label="Consider all seeds in order (no subsampling)" help="Can be used to augment -a or -k with deterministic behavior. This option significantly speeds up -a while also reducing memory consumption."/>
425 </when> 427 </when>
426 <when value="no"> 428 <when value="no">
427 <!-- do nothing --> 429 <!-- do nothing -->
428 </when> 430 </when>
429 </conditional> 431 </conditional>
1185 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with 1187 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
1186 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads 1188 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
1187 (same length, same number of mismatches allowed) at different offsets and 1189 (same length, same number of mismatches allowed) at different offsets and
1188 searches for more alignments. A read is considered to have repetitive seeds if 1190 searches for more alignments. A read is considered to have repetitive seeds if
1189 the total number of seed hits divided by the number of seeds that aligned at 1191 the total number of seed hits divided by the number of seeds that aligned at
1190 least once is greater than 300. Default: 2. 1192 least once is greater than 300. Default: 2.3
1191 1193
1194 -d/--deterministic-seeds
1195 Consider all seeds in order (no subsampling). Can be used to augment -a or -k with
1196 deterministic behavior. This option significantly speeds up -a while also reducing memory consumption.
1197 It is not however always strictly better than standalone [-a] when considering the
1198 number of repeated alignments found.
1199
1192 ----- 1200 -----
1193 1201
1194 **Paired-end options**:: 1202 **Paired-end options**::
1195 1203
1196 -I/--minins <int> 1204 -I/--minins <int>