Mercurial > repos > wolma > mimodd_aln
comparison snap_caller.xml @ 1:e76e813f615a draft
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
| author | wolma |
|---|---|
| date | Mon, 18 Dec 2017 03:38:29 -0500 |
| parents | d801b0675eb5 |
| children |
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| 0:d801b0675eb5 | 1:e76e813f615a |
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| 163 <param name="sp_max" type="integer" value="10000" | 163 <param name="sp_max" type="integer" value="10000" |
| 164 label="maximum spacing to allow between paired ends (default: 10000)" | 164 label="maximum spacing to allow between paired ends (default: 10000)" |
| 165 help="Corresponds to the second value of the SNAP option -s."/> | 165 help="Corresponds to the second value of the SNAP option -s."/> |
| 166 <param name="discard_overlapping_mates" type="text" optional="true" | 166 <param name="discard_overlapping_mates" type="text" optional="true" |
| 167 label="discard overlapping read pairs of type" | 167 label="discard overlapping read pairs of type" |
| 168 help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs." /> | 168 help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs."> |
| 169 <validator type="expression" message="only RF, FR, FF, RR or ALL are allowed as input">not value or all(token.strip(' ') in ['RF', 'FR', 'FF', 'RR', 'ALL'] for token in value.split(','))</validator> | |
| 170 </param> | |
| 169 <param name="maxdist" type="integer" value="8" | 171 <param name="maxdist" type="integer" value="8" |
| 170 label="edit distance (default: 8)" | 172 label="edit distance (default: 8)" |
| 171 help="maximum edit distance allowed per read or pair (SNAP option -d); higher values allow more divergent alignments to be found, but increase the rate of misalignments."/> | 173 help="maximum edit distance allowed per read or pair (SNAP option -d); higher values allow more divergent alignments to be found, but increase the rate of misalignments."/> |
| 172 <param name="confdiff" type="integer" value="2" | 174 <param name="confdiff" type="integer" value="2" |
| 173 label="confidence threshold (default: 2)" | 175 label="confidence threshold (default: 2)" |
| 327 <param name="sp_max" type="integer" optional="true" value="0" | 329 <param name="sp_max" type="integer" optional="true" value="0" |
| 328 label="maximum spacing to allow between paired ends" | 330 label="maximum spacing to allow between paired ends" |
| 329 help="Corresponds to the second value of the SNAP option -s."/> | 331 help="Corresponds to the second value of the SNAP option -s."/> |
| 330 <param name="discard_overlapping_mates" type="text" optional="true" value="" | 332 <param name="discard_overlapping_mates" type="text" optional="true" value="" |
| 331 label="discard overlapping read pairs of type" | 333 label="discard overlapping read pairs of type" |
| 332 help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs." /> | 334 help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs."> |
| 335 <validator type="expression" message="only RF, FR, FF, RR or ALL are allowed as input">not value or all(token.strip(' ') in ['RF', 'FR', 'FF', 'RR', 'ALL'] for token in value.split(','))</validator> | |
| 336 </param> | |
| 333 <param name="maxdist" type="integer" optional="true" value="0" | 337 <param name="maxdist" type="integer" optional="true" value="0" |
| 334 label="edit distance" | 338 label="edit distance" |
| 335 help="maximum edit distance allowed per read or pair (SNAP option -d); higher values allow more divergent alignments to be found, but increase the rate of misalignments."/> | 339 help="maximum edit distance allowed per read or pair (SNAP option -d); higher values allow more divergent alignments to be found, but increase the rate of misalignments."/> |
| 336 <param name="confdiff" type="integer" optional="true" value="" | 340 <param name="confdiff" type="integer" optional="true" value="" |
| 337 label="confidence threshold" | 341 label="confidence threshold" |