Mercurial > repos > bgruening > bismark
comparison bismark_bowtie_wrapper.xml @ 17:73508c5b4273 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sun, 24 Feb 2013 14:49:36 -0500 |
| parents | 221e740377ca |
| children | 862fb59a9a25 |
comparison
equal
deleted
inserted
replaced
| 16:c066c09db337 | 17:73508c5b4273 |
|---|---|
| 1 <tool id="bismark_bowtie" name="Bismark" version="0.7.7.2"> | 1 <tool id="bismark_bowtie" name="Bismark" version="0.7.7.3"> |
| 2 <!-- Wrapper compatible with Bismark version 0.7.7 --> | 2 <!-- Wrapper compatible with Bismark version 0.7.7 --> |
| 3 <description>bisulfite mapper (bowtie)</description> | 3 <description>bisulfite mapper (bowtie)</description> |
| 4 <!--<version_command>bismark version</version_command>--> | 4 <!--<version_command>bismark version</version_command>--> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="set_environment">SCRIPT_PATH</requirement> | 6 <requirement type="set_environment">SCRIPT_PATH</requirement> |
| 71 | 71 |
| 72 ## default 20 | 72 ## default 20 |
| 73 --seed-len $params.seed_len | 73 --seed-len $params.seed_len |
| 74 ## default 0 | 74 ## default 0 |
| 75 --seed-mismatches $params.seed_mismatches | 75 --seed-mismatches $params.seed_mismatches |
| 76 ## default 15 | 76 |
| 77 --seed-extention-attempts $params.seed_extention_attempts | |
| 78 ## default 2 | |
| 79 --max-reseed $params.max_reseed | |
| 80 | |
| 81 ## default 70 | 77 ## default 70 |
| 82 ##--maqerr $params.maqerr | 78 ##--maqerr $params.maqerr |
| 83 | 79 |
| 84 ## default unlimited | 80 ## default unlimited |
| 85 #if $params.qupto != 0: | 81 #if $params.qupto != 0: |
| 86 --qupto $params.qupto | 82 --qupto $params.qupto |
| 87 #end if | 83 #end if |
| 88 #if $params.skip_reads != 0: | 84 #if $params.skip_reads != 0: |
| 89 --skip-reads $params.skip_reads | 85 --skip-reads $params.skip_reads |
| 90 #end if | 86 #end if |
| 91 | |
| 92 ## if set, disable the original behaviour | |
| 93 $params.no_mixed | |
| 94 ## if set, disable the original behaviour | |
| 95 $params.no_discordant | |
| 96 | |
| 97 | 87 |
| 98 ###if str($params.isReportOutput) == "yes": | 88 ###if str($params.isReportOutput) == "yes": |
| 99 ## --output-report-file $report_file | 89 ## --output-report-file $report_file |
| 100 ###end if | 90 ###end if |
| 101 | 91 |
| 183 <!-- | 173 <!-- |
| 184 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." /> | 174 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." /> |
| 185 --> | 175 --> |
| 186 <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'." /> | 176 <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'." /> |
| 187 <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" /> | 177 <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" /> |
| 188 | |
| 189 <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="" /> | |
| 190 <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="" /> | |
| 191 | 178 |
| 192 <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." /> | 179 <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." /> |
| 193 <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" /> | 180 <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" /> |
| 194 <!-- output Options --> | 181 <!-- output Options --> |
| 195 <!-- | 182 <!-- |