Mercurial > repos > wolma > mimodd_aln
diff 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 |
line wrap: on
line diff
--- a/snap_caller.xml Sat Nov 11 18:18:54 2017 -0500 +++ b/snap_caller.xml Mon Dec 18 03:38:29 2017 -0500 @@ -165,7 +165,9 @@ help="Corresponds to the second value of the SNAP option -s."/> <param name="discard_overlapping_mates" type="text" optional="true" label="discard overlapping read pairs of type" - 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." /> + 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."> + <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> + </param> <param name="maxdist" type="integer" value="8" label="edit distance (default: 8)" 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."/> @@ -329,7 +331,9 @@ help="Corresponds to the second value of the SNAP option -s."/> <param name="discard_overlapping_mates" type="text" optional="true" value="" label="discard overlapping read pairs of type" - 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." /> + 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."> + <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> + </param> <param name="maxdist" type="integer" optional="true" value="0" label="edit distance" 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."/>