Mercurial > repos > rnateam > locarna_exparnap

comparison macros.xml @ 1:8723e3f8e422 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author rnateam
date Sat, 21 Jan 2017 17:38:46 -0500
parents e91e4f48875e
children e66514da3a99
comparison
equal deleted inserted replaced
0:e91e4f48875e 1:8723e3f8e422
139 #if float($Heuristics.max_bps_length_ratio) > 0.0 139 #if float($Heuristics.max_bps_length_ratio) > 0.0
140 --max-bps-length-ratio $Heuristics.max_bps_length_ratio 140 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
141 #end if 141 #end if
142 </token> 142 </token>
143 143
144 <token name="@HEURISTIC_SPARSE_ARGS@">
145 --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold
146 --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold
147
148 </token>
149
144 <token name="@CONSTRAINT_ARGS@"> 150 <token name="@CONSTRAINT_ARGS@">
145 ## -------------------- constraint parameters 151 ## -------------------- constraint parameters
146 $Constraints.lonely_pairs 152 $Constraints.lonely_pairs
147 153
148 #if $Constraints.maxBPspan != -1 154 #if $Constraints.maxBPspan != -1
230 type="float" value="0.0" min="0.0" max="10.0" 236 type="float" value="0.0" min="0.0" max="10.0"
231 label="Maximal ratio 'number of considered base pairs' by 237 label="Maximal ratio 'number of considered base pairs' by
232 'sequence length' (default: 0.0 = no effect)" /> 238 'sequence length' (default: 0.0 = no effect)" />
233 </xml> 239 </xml>
234 240
241 <xml name="common_heuristic_parameters_sparse">
242 <param name="prob_unpaired_in_loop_threshold" argument="prob-unpaired-in-loop-threshold" type="float" value="0.00005"
243 min="0.0" max="0.2"
244 label="Probability threshold for unpaired bases in loops" />
245
246 <param name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001"
247 min="0.0" max="0.2"
248 label="Probability threshold for base pairs in loops" />
249 </xml>
250
235 <xml name="in_loop_ratio_parameters"> 251 <xml name="in_loop_ratio_parameters">
236 <param name="max_uil_length_ratio" argument="max-uil-length-ratio" 252 <param name="max_uil_length_ratio" argument="max-uil-length-ratio"
237 type="float" value="0.0" min="0.0" max="10.0" 253 type="float" value="0.0" min="0.0" max="10.0"
238 label="Maximal ratio 'number considered unpaired bases in loops' by 254 label="Maximal ratio 'number considered unpaired bases in loops' by
239 'sequence length' (default: 0.0; no effect)" /> 255 'sequence length' (default: 0.0; no effect)" />
306 </data> 322 </data>
307 </xml> 323 </xml>
308 324
309 <xml name="citations"> 325 <xml name="citations">
310 <citations> 326 <citations>
311 <citation 327 <citation type="doi">10.1371/journal.pcbi.0030065</citation>
312 type="doi">10.1371/journal.pcbi.0030065</citation>
313 <citation type="doi">10.1261/rna.029041.111</citation> 328 <citation type="doi">10.1261/rna.029041.111</citation>
314 <citation type="doi">10.1093/bioinformatics/btv185</citation> 329 <citation type="doi">10.1093/bioinformatics/btv185</citation>
315 <citation type="doi">10.1186/s12859-014-0404-0</citation> 330 <citation type="doi">10.1186/s12859-014-0404-0</citation>
316 </citations> 331 </citations>
317 </xml> 332 </xml>