Mercurial > repos > rnateam > locarna_reliability_profile
comparison macros.xml @ 1:9942e1b7646c draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
author | rnateam |
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date | Fri, 13 Jan 2017 16:49:01 -0500 |
parents | 7dd1f41aee4d |
children | dd991ca3d8ce |
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0:7dd1f41aee4d | 1:9942e1b7646c |
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23 | 23 |
24 <xml name="bed_anchors"> | 24 <xml name="bed_anchors"> |
25 <conditional name="bed_anchors"> | 25 <conditional name="bed_anchors"> |
26 <param name="bed_anchors_selector" type="select" label="Anchor constraints" | 26 <param name="bed_anchors_selector" type="select" label="Anchor constraints" |
27 help="Anchor constraints in bed format specify positions of | 27 help="Anchor constraints in bed format specify positions of |
28 named anchor regions per sequence. The sequence names | 28 named anchor regions per sequence. The sequence names |
29 ('contig' names have to correspond to the fasta input | 29 ('contig' names have to correspond to the fasta input |
30 sequence names. Anchor names must be unique per sequence | 30 sequence names. Anchor names must be unique per sequence |
31 and regions of the same name for different sequences | 31 and regions of the same name for different sequences |
32 must have the same length. This constrains the alignment | 32 must have the same length. This constrains the alignment |
33 to align all regions of the same name."> | 33 to align all regions of the same name."> |
34 <option value="no">Don't load anchor constraints from bed file</option> | 34 <option value="no">Don't load anchor constraints from |
35 <option value="yes">Load anchor constraints from bed file</option> | 35 bed file</option> |
36 <option value="yes">Load anchor constraints from bed | |
37 file</option> | |
36 </param> | 38 </param> |
37 <when value="no" /> | 39 <when value="no" /> |
38 <when value="yes"> | 40 <when value="yes"> |
39 <param name="bed_anchors_file" type="data" format="tabular" | 41 <param name="bed_anchors_file" type="data" format="tabular" |
40 label="Anchor constraint specification in bed format" | 42 label="Anchor constraint specification in bed format" |
89 <param name="rnafold_temperature" argument="rnafold-temperature" | 91 <param name="rnafold_temperature" argument="rnafold-temperature" |
90 type="float" value="37.0" min="10" max="50" | 92 type="float" value="37.0" min="10" max="50" |
91 label="Temperature for RNAfold (RNAfold's -T option)" /> | 93 label="Temperature for RNAfold (RNAfold's -T option)" /> |
92 </xml> | 94 </xml> |
93 | 95 |
96 <token name="@SCORING_ARGS@"> | |
97 ## -------------------- scoring parameters | |
98 --indel $Scoring.indel | |
99 --indel-opening $Scoring.indel_opening | |
100 --struct-weight $Scoring.struct_weight | |
101 --tau $Scoring.tau | |
102 | |
103 #if str($Scoring.sequence_score.sequence_score_selector) == "match" | |
104 --match $Scoring.sequence_score.match | |
105 --mismatch $Scoring.sequence_score.mismatch | |
106 #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum" | |
107 --use-ribosum true | |
108 #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit" | |
109 --ribofit true | |
110 #end if | |
111 </token> | |
112 | |
113 <token name="@FOLDING_ARGS@"> | |
114 ## -------------------- folding parameters | |
115 #if float($Folding.rnafold_temperature) != 37.0 | |
116 --rnafold-temperature $Folding.rnafold_temperature | |
117 #end if | |
118 </token> | |
119 | |
120 <token name="@HEURISTIC_ARGS@"> | |
121 ## -------------------- heuristic parameters | |
122 -p $Heuristics.min_prob | |
123 | |
124 #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off" | |
125 --max-diff -1 | |
126 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff" | |
127 --max-diff $Heuristics.max_diff_mode.max_diff | |
128 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am" | |
129 --max-diff -1 | |
130 --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am | |
131 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln" | |
132 --max-diff $Heuristics.max_diff_mode.max_diff | |
133 --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln' | |
134 $Heuristics.max_diff_mode.max_diff_relax | |
135 #end if | |
136 | |
137 --max-diff-am $Heuristics.max_diff_am | |
138 | |
139 #if float($Heuristics.max_bps_length_ratio) > 0.0 | |
140 --max-bps-length-ratio $Heuristics.max_bps_length_ratio | |
141 #end if | |
142 </token> | |
143 | |
144 <token name="@CONSTRAINT_ARGS@"> | |
145 ## -------------------- constraint parameters | |
146 $Constraints.lonely_pairs | |
147 | |
148 #if $Constraints.maxBPspan != -1 | |
149 --maxBPspan $Constraints.maxBPspan | |
150 #end if | |
151 | |
152 $Constraints.ignore_constraints | |
153 </token> | |
154 | |
155 <token name="@STDOUT_ARGS@"> | |
156 $stdout_verbosity | |
157 | |
158 #if str($stdout_verbosity) != "--quiet": | |
159 > '$stdout' | |
160 #end if | |
161 </token> | |
162 | |
163 <xml name="max_diff_parameters_selector"> | |
164 <param name="max_diff_mode_selector" type="select" | |
165 label="Restrict alignable positions by maximum difference" | |
166 help="(max-diff*)"> | |
167 <option value="off">Off</option> | |
168 <option value="max-diff" selected="True">Maximal difference of aligned positions</option> | |
169 <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option> | |
170 <yield /> | |
171 </param> | |
172 </xml> | |
173 | |
174 <xml name="max_diff_parameters_standard_cases"> | |
175 <when value="off" /> | |
176 <when value="max-diff"> | |
177 <param name="max_diff" argument="max-diff" type="integer" | |
178 value="60" min="-1" max="300" | |
179 label="Maximal difference of aligned positions" /> | |
180 </when> | |
181 <when value="max-diff-at-am"> | |
182 <param name="max_diff_at_am" argument="max-diff-at-am" type="integer" | |
183 value="60" min="-1" max="300" | |
184 label="Maximal difference of aligned positions, | |
185 only at arc match positions" /> | |
186 </when> | |
187 </xml> | |
188 | |
189 <xml name="max_diff_parameters"> | |
190 <conditional name="max_diff_mode"> | |
191 <expand macro="max_diff_parameters_selector" /> | |
192 <expand macro="max_diff_parameters_standard_cases" /> | |
193 </conditional> | |
194 </xml> | |
195 | |
196 <xml name="max_diff_parameters_aln"> | |
197 <conditional name="max_diff_mode"> | |
198 <expand macro="max_diff_parameters_selector"> | |
199 <option value="max-diff-aln">Maximal difference to a reference alignment</option> | |
200 </expand> | |
201 <expand macro="max_diff_parameters_standard_cases" /> | |
202 <when value="max-diff-aln"> | |
203 <param name="max_diff_aln" argument="max-diff-aln" type="data" format="clustal" | |
204 label="Reference alignment" | |
205 /> | |
206 <param name="max_diff" argument="max-diff" type="integer" | |
207 value="60" min="-1" max="300" | |
208 label="Maximal difference of aligned positions" /> | |
209 <param name="max_diff_relax" argument="max-diff-relax" type="boolean" | |
210 truevalue="--max-diff-relax" falsevalue="" | |
211 checked="False" | |
212 label="Relax deviation constraints in multiple | |
213 aligmnent." | |
214 /> | |
215 </when> | |
216 </conditional> | |
217 </xml> | |
218 | |
94 <xml name="common_heuristic_parameters"> | 219 <xml name="common_heuristic_parameters"> |
95 <param name="min_prob" argument="min-prob" type="float" value="0.0005" | 220 <param name="min_prob" argument="min-prob" type="float" value="0.0005" |
96 min="0.0" max="0.2" | 221 min="0.0" max="0.2" |
97 label="Minimal / cutoff probability" /> | 222 label="Minimal / cutoff probability" /> |
98 | 223 |
99 <param name="max_diff_am" argument="max-diff-am" | 224 <param name="max_diff_am" argument="max-diff-am" |
100 type="integer" value="30" | 225 type="integer" value="30" |
101 min="-1" max="300" | 226 min="-1" max="300" |
102 label="Maximal difference for sizes of matched arcs (-1=off)" /> | 227 label="Maximal difference for sizes of matched arcs (-1=off)" /> |
103 | |
104 <param name="max_diff" argument="max-diff" type="integer" | |
105 value="60" min="-1" max="300" | |
106 label="Maximal difference for alignment traces (-1=off)" /> | |
107 | |
108 <param name="max_diff_at_am" argument="max-diff-am" type="integer" | |
109 value="-1" min="-1" max="300" | |
110 label="Maximal difference for alignment traces, only at arc match positions" /> | |
111 | 228 |
112 <param name="max_bps_length_ratio" argument="max-bps-length-ratio" | 229 <param name="max_bps_length_ratio" argument="max-bps-length-ratio" |
113 type="float" value="0.0" min="0.0" max="1.0" | 230 type="float" value="0.0" min="0.0" max="10.0" |
114 label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" /> | 231 label="Maximal ratio 'number of considered base pairs' by |
232 'sequence length' (default: 0.0 = no effect)" /> | |
233 </xml> | |
234 | |
235 <xml name="in_loop_ratio_parameters"> | |
236 <param name="max_uil_length_ratio" argument="max-uil-length-ratio" | |
237 type="float" value="0.0" min="0.0" max="10.0" | |
238 label="Maximal ratio 'number considered unpaired bases in loops' by | |
239 'sequence length' (default: 0.0; no effect)" /> | |
240 | |
241 <param name="max_bpil_length_ratio" argument="max-bpil-length-ratio" | |
242 type="float" value="0.0" min="0.0" max="10.0" | |
243 label="Maximal ratio 'number of considered base pairs in loops' | |
244 by 'sequence length' (default: 0.0; no effect)" /> | |
245 </xml> | |
246 | |
247 <xml name="exparnap_in_loop_parameters"> | |
248 <param name="prob_unpaired_in_loop_threshold" | |
249 argument="prob_unpaired_in_loop_threshold" | |
250 type="float" value="0.01" min="0.0" max="1.0" | |
251 label="Probability threshold for unpaired bases in loops" /> | |
252 <param name="prob_basepair_in_loop_threshold" | |
253 argument="prob_basepair_in_loop_threshold" | |
254 type="float" value="0.01" min="0.0" max="1.0" | |
255 label="Probability threshold for base pairs in loops" /> | |
115 </xml> | 256 </xml> |
116 | 257 |
117 <xml name="alifold_consensus_parameter"> | 258 <xml name="alifold_consensus_parameter"> |
118 <param name="alifold_consensus_dp" argument="alifold-consensus-dp" | 259 <param name="alifold_consensus_dp" argument="alifold-consensus-dp" |
119 type="boolean" checked="false" | 260 type="boolean" checked="False" |
120 truevalue="--alifold-consensus-dp" falsevalue="" | 261 truevalue="--alifold-consensus-dp" falsevalue="" |
121 label="Compute consensus dot plot by alifold" /> | 262 label="Compute consensus dot plot by alifold" /> |
122 </xml> | 263 </xml> |
123 | 264 |
124 <xml name="constraints"> | 265 <xml name="common_constraint_parameters"> |
125 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" | 266 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" |
126 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" /> | 267 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" /> |
127 <param name="maxBPspan" argument="--maxBPspan" | 268 <param name="maxBPspan" argument="--maxBPspan" |
128 type="integer" value="-1" min="-1" max="400" | 269 type="integer" value="-1" min="-1" max="400" |
129 label="Maximum basepair span by RNAfold; -1 for arbitrary span" /> | 270 label="Maximum basepair span by RNAfold; -1 for arbitrary span" /> |
131 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue="" | 272 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue="" |
132 help="Ignore all anchor and structure constraints given | 273 help="Ignore all anchor and structure constraints given |
133 in the fasta(-ish) input." /> | 274 in the fasta(-ish) input." /> |
134 </xml> | 275 </xml> |
135 | 276 |
136 <xml name="common_other_parameters"> | 277 <xml name="standard_outupt"> |
137 </xml> | |
138 | |
139 <xml name="common_outputs"> | |
140 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> | 278 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> |
141 <filter>stdout_verbosity != '--quiet'</filter> | 279 <filter>stdout_verbosity != '--quiet'</filter> |
142 </data> | 280 </data> |
281 </xml> | |
282 | |
283 <xml name="mlocarna_outputs"> | |
284 <expand macro="standard_outupt" /> | |
143 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln" | 285 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln" |
144 label="${tool.name} alignment (annotated clustal) on ${on_string}"> | 286 label="${tool.name} alignment (annotated clustal) on ${on_string}"> |
145 <filter>'clustal' in outputs</filter> | 287 <filter>'clustal' in outputs</filter> |
146 </data> | 288 </data> |
147 <data format="clustal" name="clustal_strict" | 289 <data format="clustal" name="clustal_strict" |
167 <xml name="citations"> | 309 <xml name="citations"> |
168 <citations> | 310 <citations> |
169 <citation | 311 <citation |
170 type="doi">10.1371/journal.pcbi.0030065</citation> | 312 type="doi">10.1371/journal.pcbi.0030065</citation> |
171 <citation type="doi">10.1261/rna.029041.111</citation> | 313 <citation type="doi">10.1261/rna.029041.111</citation> |
314 <citation type="doi">10.1093/bioinformatics/btv185</citation> | |
315 <citation type="doi">10.1186/s12859-014-0404-0</citation> | |
172 </citations> | 316 </citations> |
173 </xml> | 317 </xml> |
174 | 318 |
175 | 319 |
176 | 320 |