Mercurial > repos > devteam > bowtie2
changeset 34:a470b376503d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 commit 805616637ccfe14dafcffddce7935d36d8243cc1
| author | iuc |
|---|---|
| date | Thu, 05 Mar 2026 21:19:58 +0000 |
| parents | f76cbb84d67f |
| children | |
| files | bowtie2_macros.xml bowtie2_wrapper.xml |
| diffstat | 2 files changed, 11 insertions(+), 3 deletions(-) [+] |
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--- a/bowtie2_macros.xml Wed Sep 24 13:37:14 2025 +0000 +++ b/bowtie2_macros.xml Thu Mar 05 21:19:58 2026 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.5.4</token> + <token name="@TOOL_VERSION@">2.5.5</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">23.0</token> <!-- Import this at the top of your command block and then
--- a/bowtie2_wrapper.xml Wed Sep 24 13:37:14 2025 +0000 +++ b/bowtie2_wrapper.xml Thu Mar 05 21:19:58 2026 +0000 @@ -228,6 +228,7 @@ #if str( $analysis_type.effort_options.effort_options_selector ) == "yes": -D ${analysis_type.effort_options.D} -R ${analysis_type.effort_options.R} + ${analysis_type.effort_options.d} #end if #if str( $analysis_type.other_options.other_options_selector ) == "yes": ${analysis_type.other_options.non_deterministic} @@ -422,6 +423,7 @@ <when value="yes"> <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"/> <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"/> + <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."/> </when> <when value="no"> <!-- do nothing --> @@ -1187,8 +1189,14 @@ (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. - + least once is greater than 300. Default: 2.3 + + -d/--deterministic-seeds + Consider all seeds in order (no subsampling). Can be used to augment -a or -k with + deterministic behavior. This option significantly speeds up -a while also reducing memory consumption. + It is not however always strictly better than standalone [-a] when considering the + number of repeated alignments found. + ----- **Paired-end options**::