Mercurial > repos > bgruening > bismark
changeset 17:73508c5b4273 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sun, 24 Feb 2013 14:49:36 -0500 |
| parents | c066c09db337 |
| children | 862fb59a9a25 |
| files | README bismark_bowtie_wrapper.xml bismark_wrapper.py |
| diffstat | 3 files changed, 7 insertions(+), 23 deletions(-) [+] |
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--- a/README Mon Feb 18 16:07:12 2013 -0500 +++ b/README Sun Feb 24 14:49:36 2013 -0500 @@ -1,8 +1,5 @@ Bismark uses Bowtie or Bowtie2 to map the reads. -Create your reference index with bismark_genome_preparation in your -normal Bowtie2/Botwie index directory. -bismark_genome_preparation will create a Bisulfite_Genome folder directly in -your Bowtie2/Bowtie index directory. If you follow that approach you do not -need to specify or modify an extra *.loc file. -That wrapper will extract the path to the Bisulfite_Genome folder from -./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc. + +Create your reference index with bismark_genome_preparation in your normal Bowtie2/Botwie index directory. +bismark_genome_preparation will create a Bisulfite_Genome folder directly in your Bowtie2/Bowtie index directory. If you follow that approach you do not need to specify or modify an extra *.loc file. +That wrapper will extract the path to the Bisulfite_Genome folder from ./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.
--- a/bismark_bowtie_wrapper.xml Mon Feb 18 16:07:12 2013 -0500 +++ b/bismark_bowtie_wrapper.xml Sun Feb 24 14:49:36 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="bismark_bowtie" name="Bismark" version="0.7.7.2"> +<tool id="bismark_bowtie" name="Bismark" version="0.7.7.3"> <!-- Wrapper compatible with Bismark version 0.7.7 --> <description>bisulfite mapper (bowtie)</description> <!--<version_command>bismark version</version_command>--> @@ -73,11 +73,7 @@ --seed-len $params.seed_len ## default 0 --seed-mismatches $params.seed_mismatches - ## default 15 - --seed-extention-attempts $params.seed_extention_attempts - ## default 2 - --max-reseed $params.max_reseed - + ## default 70 ##--maqerr $params.maqerr @@ -89,12 +85,6 @@ --skip-reads $params.skip_reads #end if - ## if set, disable the original behaviour - $params.no_mixed - ## if set, disable the original behaviour - $params.no_discordant - - ###if str($params.isReportOutput) == "yes": ## --output-report-file $report_file ###end if @@ -186,9 +176,6 @@ <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." /> <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" /> - <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable looking for discordant alignments if it cannot find any concordant alignments" help="" /> - <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates" help="" /> - <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write ambiguous reads to an extra output file." help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." /> <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file" /> <!-- output Options -->
--- a/bismark_wrapper.py Mon Feb 18 16:07:12 2013 -0500 +++ b/bismark_wrapper.py Sun Feb 24 14:49:36 2013 -0500 @@ -178,7 +178,7 @@ if not args.bowtie2: # use bowtie specific options - additional_opts += ' --best ' + #additional_opts += ' --best ' # bug in bismark, --best is not available only --non-best, best is default if args.seed_mismatches: # --seedmms additional_opts += ' -n %s ' % args.seed_mismatches