Mercurial > repos > bgruening > bismark
diff bismark_bowtie_wrapper.xml @ 17:73508c5b4273 draft
Uploaded
author | bgruening |
---|---|
date | Sun, 24 Feb 2013 14:49:36 -0500 |
parents | 221e740377ca |
children | 862fb59a9a25 |
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--- 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 -->