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comparison macros.xml @ 2:e66514da3a99 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 13:58:16 +0000
parents 8723e3f8e422
children a80f279b4ad0
comparison
equal deleted inserted replaced
1:8723e3f8e422 2:e66514da3a99
1 <macros> 1 <macros>
2 <token name="@VERSION@">1.9.0</token> 2 <token name="@TOOL_VERSION@">1.9.2.3</token>
3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@PROFILE@">21.09</token>
3 5
4 <xml name="requirements"> 6 <xml name="requirements">
5 <requirements> 7 <requirements>
6 <requirement type="package" version="@VERSION@">locarna</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">locarna</requirement>
9 <requirement type="package" version="4.2.2">r-base</requirement>
7 </requirements> 10 </requirements>
8 </xml> 11 </xml>
9 12
10 <xml name="stdio"> 13 <xml name="stdio">
11 <stdio> 14 <stdio>
44 </when> 47 </when>
45 </conditional> 48 </conditional>
46 </xml> 49 </xml>
47 50
48 <xml name="common_scoring_parameters"> 51 <xml name="common_scoring_parameters">
49 <param name="struct_weight" argument="struct-weight" 52 <param argument="--struct-weight"
50 label="Structure weight" type="integer" 53 label="Structure weight" type="integer"
51 value="200" min="0" max="800" /> 54 value="200" min="0" max="800" />
52 <param name="indel_opening" argument="indel-opening" 55 <param argument="--indel-opening"
53 label="Indel opening score" type="integer" 56 label="Indel opening score" type="integer"
54 value="-500" max="0" min="-1500" /> 57 value="-500" max="0" min="-1500" />
55 <param argument="indel" label="Indel score" type="integer" 58 <param argument="--indel" label="Indel score" type="integer"
56 value="-350" min="-1000" max="0" /> 59 value="-350" min="-1000" max="0" />
57 <param argument="tau" type="integer" value="50" 60 <param argument="--tau" type="integer" value="50"
58 min="0" max="200" 61 min="0" max="200"
59 label="Sequence contribution at structure match in percent"/> 62 label="Sequence contribution at structure match in percent"/>
60 63
61 <conditional name="sequence_score"> 64 <conditional name="sequence_score">
62 <param name="sequence_score_selector" type="select" label="Type of sequence score contribution"> 65 <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">
76 </when> 79 </when>
77 </conditional> 80 </conditional>
78 </xml> 81 </xml>
79 82
80 <xml name="plfolding_parameters"> 83 <xml name="plfolding_parameters">
81 <param name="plfold_span" argument="--plfold-span" 84 <param argument="--plfold-span"
82 type="integer" value="150" min="-1" max="400" 85 type="integer" value="150" min="-1" max="400"
83 label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" /> 86 label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
84 87
85 <param name="plfold_winsize" argument="--plfold-winsize" 88 <param argument="--plfold-winsize"
86 type="integer" value="300" min="-1" max="800" 89 type="integer" value="300" min="-1" max="800"
87 label="Window size for local folding" /> 90 label="Window size for local folding" />
88 </xml> 91 </xml>
89 92
90 <xml name="common_folding_parameters"> 93 <xml name="common_folding_parameters">
91 <param name="rnafold_temperature" argument="rnafold-temperature" 94 <param argument="rnafold-temperature"
92 type="float" value="37.0" min="10" max="50" 95 type="float" value="37.0" min="10" max="50"
93 label="Temperature for RNAfold (RNAfold's -T option)" /> 96 label="Temperature for RNAfold (RNAfold's -T option)" />
94 </xml> 97 </xml>
95 98
96 <token name="@SCORING_ARGS@"> 99 <token name="@SCORING_ARGS@">
145 --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold 148 --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 149 --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold
147 150
148 </token> 151 </token>
149 152
153 <token name="@CONSTRAINT_ARGS_WOLP@">
154 #if $Constraints.maxBPspan != -1
155 --maxBPspan $Constraints.maxBPspan
156 #end if
157
158 $Constraints.ignore_constraints
159 </token>
150 <token name="@CONSTRAINT_ARGS@"> 160 <token name="@CONSTRAINT_ARGS@">
151 ## -------------------- constraint parameters 161 ## -------------------- constraint parameters
152 $Constraints.lonely_pairs 162 $Constraints.lonely_pairs
153 163 @CONSTRAINT_ARGS_WOLP@
154 #if $Constraints.maxBPspan != -1
155 --maxBPspan $Constraints.maxBPspan
156 #end if
157
158 $Constraints.ignore_constraints
159 </token> 164 </token>
160 165
161 <token name="@STDOUT_ARGS@"> 166 <token name="@STDOUT_ARGS@">
162 $stdout_verbosity 167 $stdout_verbosity
163 168
169 <xml name="max_diff_parameters_selector"> 174 <xml name="max_diff_parameters_selector">
170 <param name="max_diff_mode_selector" type="select" 175 <param name="max_diff_mode_selector" type="select"
171 label="Restrict alignable positions by maximum difference" 176 label="Restrict alignable positions by maximum difference"
172 help="(max-diff*)"> 177 help="(max-diff*)">
173 <option value="off">Off</option> 178 <option value="off">Off</option>
174 <option value="max-diff" selected="True">Maximal difference of aligned positions</option> 179 <option value="max-diff" selected="true">Maximal difference of aligned positions</option>
175 <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option> 180 <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option>
176 <yield /> 181 <yield />
177 </param> 182 </param>
178 </xml> 183 </xml>
179 184
180 <xml name="max_diff_parameters_standard_cases"> 185 <xml name="max_diff_parameters_standard_cases">
181 <when value="off" /> 186 <when value="off" />
182 <when value="max-diff"> 187 <when value="max-diff">
183 <param name="max_diff" argument="max-diff" type="integer" 188 <param argument="--max-diff" type="integer"
184 value="60" min="-1" max="300" 189 value="60" min="-1" max="300"
185 label="Maximal difference of aligned positions" /> 190 label="Maximal difference of aligned positions" />
186 </when> 191 </when>
187 <when value="max-diff-at-am"> 192 <when value="max-diff-at-am">
188 <param name="max_diff_at_am" argument="max-diff-at-am" type="integer" 193 <param argument="--max-diff-at-am" type="integer"
189 value="60" min="-1" max="300" 194 value="60" min="-1" max="300"
190 label="Maximal difference of aligned positions, 195 label="Maximal difference of aligned positions,
191 only at arc match positions" /> 196 only at arc match positions" />
192 </when> 197 </when>
193 </xml> 198 </xml>
204 <expand macro="max_diff_parameters_selector"> 209 <expand macro="max_diff_parameters_selector">
205 <option value="max-diff-aln">Maximal difference to a reference alignment</option> 210 <option value="max-diff-aln">Maximal difference to a reference alignment</option>
206 </expand> 211 </expand>
207 <expand macro="max_diff_parameters_standard_cases" /> 212 <expand macro="max_diff_parameters_standard_cases" />
208 <when value="max-diff-aln"> 213 <when value="max-diff-aln">
209 <param name="max_diff_aln" argument="max-diff-aln" type="data" format="clustal" 214 <param argument="--max-diff-aln" type="data" format="clustal"
210 label="Reference alignment" 215 label="Reference alignment"
211 /> 216 />
212 <param name="max_diff" argument="max-diff" type="integer" 217 <param argument="--max-diff" type="integer"
213 value="60" min="-1" max="300" 218 value="60" min="-1" max="300"
214 label="Maximal difference of aligned positions" /> 219 label="Maximal difference of aligned positions" />
215 <param name="max_diff_relax" argument="max-diff-relax" type="boolean" 220 <param argument="--max-diff-relax" type="boolean"
216 truevalue="--max-diff-relax" falsevalue="" 221 truevalue="--max-diff-relax" falsevalue=""
217 checked="False" 222 checked="False"
218 label="Relax deviation constraints in multiple 223 label="Relax deviation constraints in multiple
219 aligmnent." 224 aligmnent."
220 /> 225 />
221 </when> 226 </when>
222 </conditional> 227 </conditional>
223 </xml> 228 </xml>
224 229
225 <xml name="common_heuristic_parameters"> 230 <xml name="common_heuristic_parameters">
226 <param name="min_prob" argument="min-prob" type="float" value="0.0005" 231 <param argument="--min-prob" type="float" value="0.0005"
227 min="0.0" max="0.2" 232 min="0.0" max="0.2"
228 label="Minimal / cutoff probability" /> 233 label="Minimal / cutoff probability" />
229 234
230 <param name="max_diff_am" argument="max-diff-am" 235 <param argument="--max-diff-am"
231 type="integer" value="30" 236 type="integer" value="30"
232 min="-1" max="300" 237 min="-1" max="300"
233 label="Maximal difference for sizes of matched arcs (-1=off)" /> 238 label="Maximal difference for sizes of matched arcs (-1=off)" />
234 239
235 <param name="max_bps_length_ratio" argument="max-bps-length-ratio" 240 <param argument="--max-bps-length-ratio"
236 type="float" value="0.0" min="0.0" max="10.0" 241 type="float" value="0.0" min="0.0" max="10.0"
237 label="Maximal ratio 'number of considered base pairs' by 242 label="Maximal ratio 'number of considered base pairs' by
238 'sequence length' (default: 0.0 = no effect)" /> 243 'sequence length' (default: 0.0 = no effect)" />
239 </xml> 244 </xml>
240 245
241 <xml name="common_heuristic_parameters_sparse"> 246 <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" 247 <param argument="--prob-unpaired-in-loop-threshold" type="float" value="0.00005"
243 min="0.0" max="0.2" 248 min="0.0" max="0.2"
244 label="Probability threshold for unpaired bases in loops" /> 249 label="Probability threshold for unpaired bases in loops" />
245 250
246 <param name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001" 251 <param argument="--prob-basepair-in-loop-threshold" type="float" value="0.0001"
247 min="0.0" max="0.2" 252 min="0.0" max="0.2"
248 label="Probability threshold for base pairs in loops" /> 253 label="Probability threshold for base pairs in loops" />
249 </xml> 254 </xml>
250 255
251 <xml name="in_loop_ratio_parameters"> 256 <xml name="in_loop_ratio_parameters">
252 <param name="max_uil_length_ratio" argument="max-uil-length-ratio" 257 <param argument="--max-uil-length-ratio"
253 type="float" value="0.0" min="0.0" max="10.0" 258 type="float" value="0.0" min="0.0" max="10.0"
254 label="Maximal ratio 'number considered unpaired bases in loops' by 259 label="Maximal ratio 'number considered unpaired bases in loops' by
255 'sequence length' (default: 0.0; no effect)" /> 260 'sequence length' (default: 0.0; no effect)" />
256 261
257 <param name="max_bpil_length_ratio" argument="max-bpil-length-ratio" 262 <param argument="--max-bpil-length-ratio"
258 type="float" value="0.0" min="0.0" max="10.0" 263 type="float" value="0.0" min="0.0" max="10.0"
259 label="Maximal ratio 'number of considered base pairs in loops' 264 label="Maximal ratio 'number of considered base pairs in loops'
260 by 'sequence length' (default: 0.0; no effect)" /> 265 by 'sequence length' (default: 0.0; no effect)" />
261 </xml> 266 </xml>
262 267
263 <xml name="exparnap_in_loop_parameters"> 268 <xml name="exparnap_in_loop_parameters">
264 <param name="prob_unpaired_in_loop_threshold" 269 <param argument="--prob_unpaired_in_loop_threshold"
265 argument="prob_unpaired_in_loop_threshold"
266 type="float" value="0.01" min="0.0" max="1.0" 270 type="float" value="0.01" min="0.0" max="1.0"
267 label="Probability threshold for unpaired bases in loops" /> 271 label="Probability threshold for unpaired bases in loops" />
268 <param name="prob_basepair_in_loop_threshold" 272 <param argument="--prob_basepair_in_loop_threshold"
269 argument="prob_basepair_in_loop_threshold"
270 type="float" value="0.01" min="0.0" max="1.0" 273 type="float" value="0.01" min="0.0" max="1.0"
271 label="Probability threshold for base pairs in loops" /> 274 label="Probability threshold for base pairs in loops" />
272 </xml> 275 </xml>
273 276
274 <xml name="alifold_consensus_parameter"> 277 <xml name="alifold_consensus_parameter">
275 <param name="alifold_consensus_dp" argument="alifold-consensus-dp" 278 <param argument="--alifold-consensus-dp"
276 type="boolean" checked="False" 279 type="boolean" checked="False"
277 truevalue="--alifold-consensus-dp" falsevalue="" 280 truevalue="--alifold-consensus-dp" falsevalue=""
278 label="Compute consensus dot plot by alifold" /> 281 label="Compute consensus dot plot by alifold" />
279 </xml> 282 </xml>
280 283
281 <xml name="common_constraint_parameters"> 284 <xml name="common_constraint_parameters_woLP">
282 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" 285 <yield/>
283 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" /> 286 <param argument="--maxBPspan"
284 <param name="maxBPspan" argument="--maxBPspan"
285 type="integer" value="-1" min="-1" max="400" 287 type="integer" value="-1" min="-1" max="400"
286 label="Maximum basepair span by RNAfold; -1 for arbitrary span" /> 288 label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
287 <param name="ignore_constraints" argument="ignore-constraints" 289 <param argument="--ignore-constraints"
288 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue="" 290 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
289 help="Ignore all anchor and structure constraints given 291 help="Ignore all anchor and structure constraints given
290 in the fasta(-ish) input." /> 292 in the fasta(-ish) input." />
291 </xml> 293 </xml>
292 294
295 <xml name="common_constraint_parameters">
296 <expand macro="common_constraint_parameters_woLP">
297 <param argument="--noLP" name="lonely_pairs" type="boolean" truevalue="" falsevalue="--noLP"
298 checked="true" label="Allow lonely base-pairs"/>
299 </expand>
300 </xml>
301
293 <xml name="standard_outupt"> 302 <xml name="standard_outupt">
294 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> 303 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout">
295 <filter>stdout_verbosity != '--quiet'</filter> 304 <filter>stdout_verbosity != '--quiet'</filter>
296 </data> 305 </data>
297 </xml> 306 </xml>
298 307
299 <xml name="mlocarna_outputs"> 308 <xml name="mlocarna_outputs">
300 <expand macro="standard_outupt" /> 309 <expand macro="standard_outupt" />
301 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln" 310 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
302 label="${tool.name} alignment (annotated clustal) on ${on_string}"> 311 label="${tool.name} on ${on_string}: alignment (annotated clustal)">
303 <filter>'clustal' in outputs</filter> 312 <filter>'clustal' in outputs</filter>
304 </data> 313 </data>
305 <data format="clustal" name="clustal_strict" 314 <data format="clustal" name="clustal_strict"
306 from_work_dir="mlocarna_results/results/result.strict-aln" 315 from_work_dir="mlocarna_results/results/result.strict-aln"
307 label="${tool.name} alignment (clustal) on ${on_string}"> 316 label="${tool.name} on ${on_string}: alignment (clustal)">
308 <filter>'clustal_strict' in outputs</filter> 317 <filter>'strict' in outputs</filter>
309 </data> 318 </data>
310 <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk" 319 <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
311 label="${tool.name} alignment (stockholm) on ${on_string}"> 320 label="${tool.name} on ${on_string}: alignment (stockholm)">
312 <filter>'stockholm' in outputs</filter> 321 <filter>'stockholm' in outputs</filter>
313 </data> 322 </data>
314 <data format="txt" name="pp" 323 <data format="txt" name="pp"
315 from_work_dir="mlocarna_results/results/result.pp" 324 from_work_dir="mlocarna_results/results/result.pp"
316 label="${tool.name} alignment (PP 2.0) on ${on_string}"> 325 label="${tool.name} on ${on_string}: alignment (PP 2.0)">
317 <filter>'pp' in outputs</filter> 326 <filter>'pp' in outputs</filter>
318 </data> 327 </data>
319 <data format="tar.gz" name="mlocarna_results_tgz" 328 <data format="tar.gz" name="mlocarna_results_tgz"
320 label="${tool.name} results archive on ${on_string}"> 329 label="${tool.name} on ${on_string}: results archive">
321 <filter>'mlocarna_results' in outputs</filter> 330 <filter>'mlocarna_results' in outputs</filter>
322 </data> 331 </data>
323 </xml> 332 </xml>
324 333
325 <xml name="citations"> 334 <xml name="citations">
328 <citation type="doi">10.1261/rna.029041.111</citation> 337 <citation type="doi">10.1261/rna.029041.111</citation>
329 <citation type="doi">10.1093/bioinformatics/btv185</citation> 338 <citation type="doi">10.1093/bioinformatics/btv185</citation>
330 <citation type="doi">10.1186/s12859-014-0404-0</citation> 339 <citation type="doi">10.1186/s12859-014-0404-0</citation>
331 </citations> 340 </citations>
332 </xml> 341 </xml>
333
334
335
336 </macros> 342 </macros>
337 343