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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
author rnateam
date Tue, 21 Feb 2017 04:59:09 -0500
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1 <tool id="intarna" name="IntaRNA" version="2.0.0">
2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
3 <macros>
4 <macro name="query_macro">
5 <param name="_query" argument="--query" format="fasta" type="data" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" />
6 <conditional name="qAcc_cond">
7 <param argument="--qAcc" type="select" label="Accessibility computation" help="">
8 <option value="N">No accessibility contributions ('N')</option>
9 <option value="C" selected="true">Computation of accessibilities ('C')</option>
10 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
11 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
12 </param>
13 <when value="N"/>
14 <when value="C"/>
15 <when value="P">
16 <param argument="--qAccFile" format="text" type="data" label="Accessibility computation" help="" />
17 </when>
18 <when value="E">
19 <param argument="--qAccFile" format="text" type="data" label="Accessibility computation" help="" />
20 </when>
21 </conditional>
22 <param argument="--qAccW" type="integer" value="150" min="0" max="99999"
23 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
24 <param argument="--qAccL" type="integer" value="100" min="0" max="99999"
25 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW'"/>
26 </macro>
27 <macro name="target_macro">
28 <param name="_target" argument="--target" format="fasta" type="data" label="Target sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" />
29 <conditional name="tAcc_cond">
30 <param argument="--tAcc" type="select" label="Accessibility computation" help="">
31 <option value="N">No accessibility contributions ('N')</option>
32 <option value="C" selected="true">Computation of accessibilities ('C')</option>
33 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
34 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
35 </param>
36 <when value="N"/>
37 <when value="C"/>
38 <when value="P">
39 <param argument="--tAccFile" format="text" type="data" label="The file to be parsed" help="... for accessibility computation" />
40 </when>
41 <when value="E">
42 <param argument="--tAccFile" format="text" type="data" label="Accessibility computation" help="" />
43 </when>
44 </conditional>
45 <param argument="--tAccW" type="integer" value="150" min="0" max="99999"
46 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
47 <param argument="--tAccL" type="integer" value="100" min="0" max="99999"
48 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'tAccW'"/>
49 </macro>
50 <macro name="seed_macro">
51 <param argument="--noSeed" truevalue="--noSeed" falsevalue="" checked="False" type="boolean"
52 label="Disable seed constraint entirely for computation" help=""/>
53 <param argument="--seedBP" type="integer" value="7" min="2" max="20" label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/>
54 <param argument="--seedMaxUP" type="integer" value="0" min="0" max="20"
55 label="Max. overall number of unpaired bases (query+target)" help=""/>
56 </macro>
57 <macro name="interaction_macro">
58 <param argument="--mode" type="select" label="Prediction mode" help="">
59 <option value="H" selected="true">Heuristic (fast and low memory)</option>
60 <option value="M">Exact and low memory</option>
61 <option value="E">Exact (high memory)</option>
62 </param>
63 </macro>
64 <macro name="output_macro">
65 <param argument="--outMode" type="select" label="Output Mode" help="">
66 <option value="N">Normal output (ASCII char + energy)</option>
67 <option value="D">Detailed output (ASCII char + energy/position details)</option>
68 <option value="C" selected="true">CSV output (see --outCsvCols)</option>
69 <option value="1">backward compatible IntaRNA v1.* normal output</option>
70 <option value="O">backward compatible IntaRNA v1.* detailed output</option>
71 </param>
72
73
74 <param argument="--outCsvCols" type="text" optional="true"
75 label="Comma separated list of CSV column IDs to print" help="An empty argument prints all possible columns from the following available ID list: [id1], [id2], [seq1], [seq2], [subseq1], [subseq2], [subseqDP], [subseqDB], [start1], [end1], [start2], [end2], [hybridDP], [hybridDB], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2]"/>
76 <param argument="--outNumber" type="integer" value="1" min="0" max="1000"
77 label="Max. number of predictions per query/target pair" help="Number of optimal and suboptimal interaction to predict per query-target pair"/>
78 <param argument="--outOverlap" type="select" label="Overlapping of suboptimal predictions" help="Whether or not interactions can overlap">
79 <option value="N" >in none of the sequences</option>
80 <option value="T">in the target only</option>
81 <option value="Q" selected="true">in the query only</option>
82 <option value="B">in both sequences</option>
83 </param>
84 </macro>
85 </macros>
86 <requirements>
87 <requirement type="package" version="2.0.0">intarna</requirement>
88 </requirements>
89 <stdio>
90 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
91 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
92 </stdio>
93 <version_command>IntaRNA --version</version_command>
94 <command>
95 <![CDATA[
96 IntaRNA
97 #if $advancedOptions.advancedSelector == "advanced"
98 ## Query parameters
99 --query '$advancedOptions.query._query'
100 --qAcc $advancedOptions.query.qAcc_cond.qAcc
101 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
102 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
103 #end if
104 --qAccW $advancedOptions.query.qAccW
105 --qAccL $advancedOptions.query.qAccL
106 ## #if $advancedOptions.query.qAccConstr <> "."
107 ## --qAccConstr $advancedOptions.query.qAccConstr
108 ## #end if
109 --qIntLoopMax $advancedOptions.query.qIntLoopMax
110 #if $advancedOptions.query.qRegion
111 --qRegion '$advancedOptions.query.qRegion'
112 #end if
113
114 ## Target param.
115 --target '$advancedOptions.target._target'
116 --tAcc $advancedOptions.target.tAcc_cond.tAcc
117 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
118 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
119 #end if
120 --tAccW $advancedOptions.target.tAccW
121 --tAccL $advancedOptions.target.tAccL
122 ## #if $advancedOptions.target.tAccConstr <> "."
123 ## --tAccConstr $advancedOptions.target.tAccConstr
124 ## #end if
125 --tIntLoopMax $advancedOptions.target.tIntLoopMax
126 #if $advancedOptions.target.tRegion
127 --tRegion '$advancedOptions.target.tRegion'
128 #end if
129
130 ## Seed param.
131 --noSeed $advancedOptions.seed.noSeed
132 --seedBP $advancedOptions.seed.seedBP
133 --seedMaxUP $advancedOptions.seed.seedMaxUP
134 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
135 --seedTMaxUP $advancedOptions.seed.seedTMaxUP
136 --seedMaxE $advancedOptions.seed.seedMaxE
137 --seedMinPu $advancedOptions.seed.seedMinPu
138 --seedQRange '$advancedOptions.seed.seedQRange'
139 --seedTRange '$advancedOptions.seed.seedTRange'
140
141 ## Interaction param.
142 --mode $advancedOptions.interaction.mode
143 --pred $advancedOptions.interaction.pred
144 --energy $advancedOptions.interaction.energy
145 #if $advancedOptions.interaction.energyVRNA
146 --energyVRNA '$advancedOptions.interaction.energyVRNA'
147 #end if
148 --temperature $advancedOptions.interaction.temperature
149
150 ##Output param.
151 --out ./temp_tabular_output
152 --outMode $advancedOptions.output.outMode
153 --outNumber $advancedOptions.output.outNumber
154 --outOverlap $advancedOptions.output.outOverlap
155 --outMaxE $advancedOptions.output.outMaxE
156 --outDeltaE $advancedOptions.output.outDeltaE
157 #if $advancedOptions.output.outCsvCols
158 --outCsvCols '$advancedOptions.output.outCsvCols'
159 #end if
160 #if $advancedOptions.output.add_output_cond.selector == "add"
161 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
162 #for j in $advancedOptions.output.add_output_cond.add_output.value:
163 --$j $getVar($j)
164 #end for
165 #end if
166 #end if
167
168 #elif $advancedOptions.advancedSelector == "basic"
169 ## Query parameters
170 --query '$advancedOptions.query._query'
171 --qAcc $advancedOptions.query.qAcc_cond.qAcc
172 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
173 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
174 #end if
175 --qAccW $advancedOptions.query.qAccW
176 --qAccL $advancedOptions.query.qAccL
177
178 ## Target param.
179 --target '$advancedOptions.target._target'
180 --tAcc $advancedOptions.target.tAcc_cond.tAcc
181 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
182 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
183 #end if
184 --tAccW $advancedOptions.target.tAccW
185 --tAccL $advancedOptions.target.tAccL
186
187 ## Seed param.
188 --noSeed $advancedOptions.seed.noSeed
189 --seedBP $advancedOptions.seed.seedBP
190 --seedMaxUP $advancedOptions.seed.seedMaxUP
191
192 ## Interaction param.
193 --mode $advancedOptions.interaction.mode
194
195 ##Output param.
196 --out ./temp_tabular_output
197 --outMode $advancedOptions.output.outMode
198 --outNumber $advancedOptions.output.outNumber
199 --outOverlap $advancedOptions.output.outOverlap
200 #if $advancedOptions.output.outCsvCols
201 --outCsvCols '$advancedOptions.output.outCsvCols'
202 #end if
203 #end if
204 && sed 's/\t/ /g' ./temp_tabular_output > ./temp_output_no_tabs
205 && sed 's/;/\t/g' ./temp_output_no_tabs > '$outfile'
206
207 ]]>
208 </command>
209 <inputs>
210
211 <conditional name="advancedOptions">
212 <param name="advancedSelector" type="select" label="Options">
213 <option value="basic">Basic Options</option>
214 <option value="advanced">Advanced Options</option>
215 </param>
216 <when value="advanced">
217 <section name="query" title="Query Parameters" expanded="True">
218 <expand macro="query_macro"/>
219 <!--
220 <param name="qAccConstr" type="select" label="Structure constraint for each sequence position" help="">
221 <option value="." selected="true">No constraint</option>
222 <option value="x">Unpaired</option>
223 <option value="b">Blocked positions are excluded from interaction prediction and considered unpaired </option>
224 </param>
225 -->
226 <param argument="--qIntLoopMax" type="integer" value="16" min="0" max="30"
227 label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the query"/>
228 <param argument="--qRegion" type="text" optional="true" label="Query regions to be considered for interaction prediction"
229 help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" />
230 </section>
231 <section name="target" title="Target Parameters" expanded="True">
232 <expand macro="target_macro"/>
233 <!-- <param name="tAccConstr" type="select" label="Structure constraint for each sequence position" help="">
234 <option value="." selected="true">No constraint</option>
235 <option value="x">Unpaired</option>
236 <option value="b">Blocked.blocked positions are excluded from interaction prediction and considered unpaired </option>
237 </param>
238 -->
239
240 <param argument="--tIntLoopMax" type="integer" value="16" min="0" max="30"
241 label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the target"/>
242 <param argument="--tRegion" type="text" optional="true" label="Target regions to be considered for interaction prediction"
243 help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" />
244 </section>
245 <section name="seed" title="Seed Parameters">
246 <expand macro="seed_macro"/>
247 <param argument="--seedQMaxUP" type="integer" value="-1" min="-1" max="20"
248 label="Max. number of unpaired bases within the query's seed region" help=""/>
249 <param argument="--seedTMaxUP" type="integer" value="-1" min="-1" max="20"
250 label="Max. number of unpaired bases within the target's seed region" help=""/>
251 <param argument="--seedMaxE" type="integer" value="0" min="-999" max="999"
252 label="Max. energy a seed region may have" help=""/>
253 <param argument="--seedMinPu" type="float" value="0" min="0" max="1"
254 label="Min. unpaired probability (per sequence)" help=""/>
255
256 <param argument="--seedQRange" type="text" value=""
257 label="Interval(s) in the query to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
258 <param argument="--seedTRange" type="text" value=""
259 label="Interval(s) in the target to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
260 </section>
261 <section name="interaction" title="Interaction Parameters">
262 <expand macro="interaction_macro"/>
263 <param argument="--pred" type="select" label="Prediction target" help="Sets what to optimize for">
264 <option value="S" selected="true">Single-site minimum-free-energy interaction</option>
265 <option value="P">Single-site maximum-probability interaction</option>
266 </param>
267 <param argument="--energy" type="select" label="Energy computation" help="">
268 <!-- <option value="B">Base pair == -1 ()</option> -->
269 <option value="V" selected="true">VRNA-based computation</option>
270 </param>
271 <param argument="--energyVRNA" type="data" format="*" optional="true"
272 label="Energy parameter file of VRNA package" help="If not provided, the default parameter set of the linked Vienna RNA package is used."/>
273 <param argument="--temperature" type="integer" value="37" min="0" max="100"
274 label="Temperature [°C]" help="VRNA energy parameters"/>
275 </section>
276 <section name="output" title="Output Options">
277 <expand macro="output_macro"/>
278 <param argument="--outMaxE" type="float" value="0"
279 label="Max. absolute energy of an interaction" help="Only interactions with E &#8804; maxE are reported"/>
280 <param argument="--outDeltaE" type="float" value="100"
281 label="Max. delta energy above mfe of an interaction" help="suboptimal output: only interactions with E &#8804; (minE+deltaE) are reported"/>
282
283 <conditional name="add_output_cond">
284 <param name="selector" type="select" label="Additional output files">
285 <option value="add">Output additional files</option>
286 <option value="none" selected="true">Don't output additional files</option>
287 </param>
288 <when value="add">
289 <param name="add_output" type="select" display="checkboxes" multiple="True"
290 label="Additional output files" help="Written in a format similar to RNAplfold unpaired probability output.">
291 <option value="outQAccFile" selected="true">The query's ED values (--outQAccFile)</option>
292 <option value="outTAccFile">The target's ED values (--outTAccFile) </option>
293 <option value="outQPuFile">The query's unpaired probabilities used for ED values (--outQPuFile) </option>
294 <option value="outTPuFile">The target's unpaired probabilities used for ED values (--outTPuFile)</option>
295 </param>
296 </when>
297 <when value="none"/>
298 </conditional>
299
300 </section>
301 </when>
302 <when value="basic">
303 <section name="query" title="Query Parameters" expanded="True">
304 <expand macro="query_macro"/>
305 </section>
306 <section name="target" title="Target Parameters" expanded="True">
307 <expand macro="target_macro"/>
308 </section>
309 <section name="seed" title="Seed Parameters">
310 <expand macro="seed_macro"/>
311 </section>
312 <section name="interaction" title="Interaction Parameters">
313 <expand macro="interaction_macro"/>
314 </section>
315 <section name="output" title="Output Options">
316 <expand macro="output_macro"/>
317 </section>
318 </when>
319 </conditional>
320 </inputs>
321 <outputs>
322 <data name="outfile" format="text" label="IntaRNA on ${on_string}">
323 <change_format>
324 <when input="advancedOptions.output.outMode" value="C" format="tabular" />
325 </change_format>
326 </data>
327 <data name="outQAccFile" format="text" label="Query's ED values, on ${on_string}">
328 <filter>
329 ((
330 advancedOptions['advancedSelector'] == "advanced" and
331 advancedOptions['output']['add_output_cond']['selector'] == "add" and
332 'outQAccFile' in advancedOptions['output']['add_output_cond']['add_output']
333 ))
334 </filter>
335 </data>
336 <data name="outTAccFile" format="text" label="Target's ED values, on ${on_string}">
337 <filter>
338 ((
339 advancedOptions['advancedSelector'] == "advanced" and
340 advancedOptions['output']['add_output_cond']['selector'] == "add" and
341 'outTAccFile' in advancedOptions['output']['add_output_cond']['add_output']
342 ))
343 </filter>
344 </data>
345 <data name="outQPuFile" format="text" label="Query's unpaired probabilities used for ED values, on ${on_string}">
346 <filter>
347 ((
348 advancedOptions['advancedSelector'] == "advanced" and
349 advancedOptions['output']['add_output_cond']['selector'] == "add" and
350 'outQPuFile' in advancedOptions['output']['add_output_cond']['add_output']
351 ))
352 </filter>
353 </data>
354 <data name="outTPuFile" format="text" label="Target's unpaired probabilities used for ED values, on ${on_string}">
355 <filter>
356 ((
357 advancedOptions['advancedSelector'] == "advanced" and
358 advancedOptions['output']['add_output_cond']['selector'] == "add" and
359 'outTPuFile' in advancedOptions['output']['add_output_cond']['add_output']
360 ))
361 </filter>
362 </data>
363 </outputs>
364 <tests>
365 <test>
366 <conditional name="advancedOptions">
367 <param name="advancedSelector" value="basic"/>
368 <section name="query">
369 <param name="_query" value="intarna_query.fa" />
370 </section>
371 <section name="target">
372 <param name="_target" value="intarna_target.fa"/>
373 </section>
374 </conditional>
375 <output name="outfile" file="intarna_result.tabular"/>
376 </test>
377 </tests>
378
379 <help>
380 <![CDATA[
381
382 **What it does**
383
384 Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites
385
386 During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches.
387
388 IntaRNA, developed by `Prof. Backofen's bioinformatics group at Freiburg University <http://www.bioinf.uni-freiburg.de/>`_, is a general and fast approach to the prediction of RNA-RNA interactions incorporating both the accessibility of interacting sites as well as the existence of a user-definable seed interaction. We successfully applied IntaRNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs.
389
390 .. class:: infomark
391
392 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information.
393
394
395 **Input**
396
397
398
399 RNA sequences in *FASTA* format
400
401
402 **Output**
403
404 RNA-RNA interaction information in CSV format and additional information/files on demand
405
406 ]]>
407
408 </help>
409
410 <citations>
411 <citation type="doi">10.1093/nar/gku359</citation>
412 <citation type="doi">10.1093/bioinformatics/btn544</citation>
413 </citations>
414
415 </tool>