| Previous changeset 0:e91e4f48875e (2017-01-13) Next changeset 2:e66514da3a99 (2022-12-05) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 |
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modified:
macros.xml |
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| diff -r e91e4f48875e -r 8723e3f8e422 macros.xml --- a/macros.xml Fri Jan 13 16:49:16 2017 -0500 +++ b/macros.xml Sat Jan 21 17:38:46 2017 -0500 |
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| @@ -141,6 +141,12 @@ #end if </token> + <token name="@HEURISTIC_SPARSE_ARGS@"> + --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold + --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold + + </token> + <token name="@CONSTRAINT_ARGS@"> ## -------------------- constraint parameters $Constraints.lonely_pairs @@ -232,6 +238,16 @@ 'sequence length' (default: 0.0 = no effect)" /> </xml> + <xml name="common_heuristic_parameters_sparse"> + <param name="prob_unpaired_in_loop_threshold" argument="prob-unpaired-in-loop-threshold" type="float" value="0.00005" + min="0.0" max="0.2" + label="Probability threshold for unpaired bases in loops" /> + + <param name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001" + min="0.0" max="0.2" + label="Probability threshold for base pairs in loops" /> + </xml> + <xml name="in_loop_ratio_parameters"> <param name="max_uil_length_ratio" argument="max-uil-length-ratio" type="float" value="0.0" min="0.0" max="10.0" @@ -308,8 +324,7 @@ <xml name="citations"> <citations> - <citation - type="doi">10.1371/journal.pcbi.0030065</citation> + <citation type="doi">10.1371/journal.pcbi.0030065</citation> <citation type="doi">10.1261/rna.029041.111</citation> <citation type="doi">10.1093/bioinformatics/btv185</citation> <citation type="doi">10.1186/s12859-014-0404-0</citation> |