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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
author bgruening
date Wed, 18 Sep 2024 19:42:08 +0000
parents 0377acb3f91b
children
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15:0377acb3f91b 16:f5d850723e63
1 <tool id="intarna" name="IntaRNA" version="3.4.0"> 1 <tool id="intarna" name="IntaRNA" version="3.4.1" profile="23.0">
2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description> 2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
3 <macros> 3 <macros>
4 <macro name="query_macro"> 4 <macro name="query_macro">
5 <param argument="--query" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" /> 5 <param argument="--query" type="data" format="fasta" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format"/>
6 <conditional name="qAcc_cond"> 6 <conditional name="qAcc_cond">
7 <param argument="--qAcc" help="" label="Accessibility computation" type="select"> 7 <param argument="--qAcc" type="select" label="Accessibility computation" help="">
8 <option value="N">No accessibility contributions ('N')</option> 8 <option value="N">No accessibility contributions ('N')</option>
9 <option selected="true" value="C">Computation of accessibilities ('C')</option> 9 <option selected="true" value="C">Computation of accessibilities ('C')</option>
10 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</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> 11 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
12 </param> 12 </param>
13 <when value="N" /> 13 <when value="N"/>
14 <when value="C" /> 14 <when value="C"/>
15 <when value="P"> 15 <when value="P">
16 <param argument="--qAccFile" format="txt" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA" label="RNAplfold unpaired probability data" type="data" /> 16 <param argument="--qAccFile" type="data" format="txt" label="RNAplfold unpaired probability data" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA"/>
17 </when> 17 </when>
18 <when value="E"> 18 <when value="E">
19 <param argument="--qAccFile" format="txt" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA" label="IntaRNA accessibility energy penalties (ED terms)" type="data" /> 19 <param argument="--qAccFile" type="data" format="txt" label="IntaRNA accessibility energy penalties (ED terms)" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA"/>
20 </when> 20 </when>
21 </conditional> 21 </conditional>
22 <param argument="--qAccW" help="... for query accessibility computation. Set to 0 to use full sequence length" label="Max. interaction length" max="99999" min="0" type="integer" value="150" /> 22 <param argument="--qAccW" type="integer" min="0" max="99999" value="150" label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
23 <param argument="--qAccL" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW'" label="Max. loop length" max="99999" min="0" type="integer" value="100" /> 23 <param argument="--qAccL" type="integer" min="0" max="99999" value="100" label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW"/>
24 </macro> 24 </macro>
25 <macro name="target_macro"> 25 <macro name="target_macro">
26 <param argument="--target" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Target sequence(s)" name="target" type="data" /> 26 <param argument="--target" type="data" format="fasta" label="Target sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format"/>
27 <conditional name="tAcc_cond"> 27 <conditional name="tAcc_cond">
28 <param argument="--tAcc" help="" label="Accessibility computation" type="select"> 28 <param argument="--tAcc" type="select" label="Accessibility computation" help="">
29 <option value="N">No accessibility contributions ('N')</option> 29 <option value="N">No accessibility contributions ('N')</option>
30 <option selected="true" value="C">Computation of accessibilities ('C')</option> 30 <option selected="true" value="C">Computation of accessibilities ('C')</option>
31 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option> 31 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
32 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option> 32 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
33 </param> 33 </param>
34 <when value="N" /> 34 <when value="N"/>
35 <when value="C" /> 35 <when value="C"/>
36 <when value="P"> 36 <when value="P">
37 <param argument="--tAccFile" format="txt" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA" label="RNAplfold unpaired probability data" type="data" /> 37 <param argument="--tAccFile" type="data" format="txt" label="RNAplfold unpaired probability data" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA"/>
38 </when> 38 </when>
39 <when value="E"> 39 <when value="E">
40 <param argument="--tAccFile" format="txt" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA" label="IntaRNA accessibility energy penalties (ED terms)" type="data" /> 40 <param argument="--tAccFile" type="data" format="txt" label="IntaRNA accessibility energy penalties (ED terms)" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA"/>
41 </when> 41 </when>
42 </conditional> 42 </conditional>
43 <param argument="--tAccW" help="... for target accessibility computation. Set to 0 to use full sequence length" label="Max. interaction length" max="99999" min="0" type="integer" value="150" /> 43 <param argument="--tAccW" type="integer" min="0" max="99999" value="150" label="Max. interaction length" help="... for target accessibility computation. Set to 0 to use full sequence length"/>
44 <param argument="--tAccL" help="... for target accessibility computation. 0 defaults to sliding window size 'tAccW'" label="Max. loop length" max="99999" min="0" type="integer" value="100" /> 44 <param argument="--tAccL" type="integer" min="0" max="99999" value="100" label="Max. loop length" help="... for target accessibility computation. 0 defaults to sliding window size 'tAccW"/>
45 </macro> 45 </macro>
46 <macro name="seed_macro"> 46 <macro name="seed_macro">
47 <param argument="--noSeed" checked="false" falsevalue="" help="" label="Disable seed constraint entirely for computation" truevalue="--noSeed" type="boolean" /> 47 <param argument="--noSeed" type="boolean" truevalue="--noSeed" falsevalue="" checked="false" label="Disable seed constraint entirely for computation" help=""/>
48 <param argument="--seedBP" help="number of inter-molecular base pairs within the seed region" label="Min. number of basepairs in seed" max="20" min="2" type="integer" value="7" /> 48 <param argument="--seedBP" type="integer" min="2" max="20" value="7" label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/>
49 <param argument="--seedMaxUP" help="Maximal number of unpaired seed bases both in query and target" label="Max. overall number of unpaired bases in seed" max="10" min="0" type="integer" value="0" /> 49 <param argument="--seedMaxUP" type="integer" min="0" max="10" value="0" label="Max. overall number of unpaired bases in seed" help="Maximal number of unpaired seed bases both in query and target"/>
50 </macro> 50 </macro>
51 <macro name="interaction_macro"> 51 <macro name="interaction_macro">
52 <param argument="--mode" help="" label="Prediction mode" type="select"> 52 <param argument="--mode" type="select" label="Prediction mode" help="">
53 <option selected="true" value="H">Heuristic ('H')</option> 53 <option selected="true" value="H">Heuristic ('H')</option>
54 <option value="M">Exact but slow ('M')</option> 54 <option value="M">Exact but slow ('M')</option>
55 </param> 55 </param>
56 </macro> 56 </macro>
57 <macro name="output_macro"> 57 <macro name="output_macro">
58 <param argument="--outCsvCols" 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], [hybridDPfull], [hybridDBfull], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [E_hybrid], [E_norm], [E_hybridNorm], [E_add], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2], [w], [Eall], [Zall], [P_E]" label="Comma separated list of CSV column IDs to print" type="text" value="id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E" /> 58 <param argument="--outCsvCols" type="text" value="id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E" 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], [hybridDPfull], [hybridDBfull], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [E_hybrid], [E_norm], [E_hybridNorm], [E_add], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2], [w], [Eall], [Zall], [P_E]"/>
59 <param argument="--outCsvSort" help="One of the column IDs to be printed that is used to sort the CSV table output" label="Sort CSV output for the given column label from CSV column IDs to print" type="text" value="E" /> 59 <param argument="--outCsvSort" type="text" value="E" label="Sort CSV output for the given column label from CSV column IDs to print" help="One of the column IDs to be printed that is used to sort the CSV table output"/>
60 <param argument="--outNumber" help="Number of optimal and suboptimal interaction to predict per query-target pair" label="Max. number of predictions per query/target pair" max="1000" min="0" type="integer" value="1" /> 60 <param argument="--outNumber" type="integer" min="0" max="1000" value="1" label="Max. number of predictions per query/target pair" help="Number of optimal and suboptimal interaction to predict per query-target pair"/>
61 <param argument="--outOverlap" help="Whether or not interactions can overlap" label="Overlapping of suboptimal predictions" type="select"> 61 <param argument="--outOverlap" type="select" label="Overlapping of suboptimal predictions" help="Whether or not interactions can overlap">
62 <option value="N">in none of the sequences</option> 62 <option value="N">in none of the sequences</option>
63 <option value="T">in the target only</option> 63 <option value="T">in the target only</option>
64 <option selected="true" value="Q">in the query only</option> 64 <option selected="true" value="Q">in the query only</option>
65 <option value="B">in both sequences</option> 65 <option value="B">in both sequences</option>
66 </param> 66 </param>
67 <param argument="--outPairwise" checked="false" falsevalue="" help="" label="Enables pairwise sequence processing, i.e. interactions are only computed for each corresponding query-target pair (same index) instead of all-vs-all" truevalue="--outPairwise" type="boolean" /> 67 <param argument="--outPairwise" type="boolean" truevalue="--outPairwise" falsevalue="" checked="false" label="Enables pairwise sequence processing, i.e. interactions are only computed for each corresponding query-target pair (same index) instead of all-vs-all" help=""/>
68 </macro> 68 </macro>
69 </macros> 69 </macros>
70 <requirements> 70 <requirements>
71 <requirement type="package" version="3.4.0">intarna</requirement> 71 <requirement type="package" version="3.4.1">intarna</requirement>
72 </requirements> 72 </requirements>
73 <version_command>IntaRNA --version</version_command> 73 <version_command>IntaRNA --version</version_command>
74 <command detect_errors="exit_code"><![CDATA[ 74 <command detect_errors="exit_code"><![CDATA[
75 75
76 IntaRNA 76 IntaRNA
180 #end if 180 #end if
181 ]]> 181 ]]>
182 </command> 182 </command>
183 <inputs> 183 <inputs>
184 <conditional name="advancedOptions"> 184 <conditional name="advancedOptions">
185 <param label="Options" name="advancedSelector" type="select"> 185 <param name="advancedSelector" type="select" label="Options">
186 <option value="basic">Basic Options</option> 186 <option value="basic">Basic Options</option>
187 <option value="advanced">Advanced Options</option> 187 <option value="advanced">Advanced Options</option>
188 </param> 188 </param>
189 <when value="advanced"> 189 <when value="advanced">
190 <section expanded="True" name="query" title="Query Parameters"> 190 <section expanded="True" name="query" title="Query Parameters">
191 <expand macro="query_macro" /> 191 <expand macro="query_macro"/>
192 <param argument="--qIntLoopMax" help="... to be considered in interactions within the query" label="Maximal number of unpaired bases between neighbored interacting bases" max="30" min="0" type="integer" value="16" /> 192 <param argument="--qIntLoopMax" type="integer" min="0" max="30" value="16" label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the query"/>
193 <param argument="--qRegion" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" label="Query regions to be considered for interaction prediction" optional="true" type="text" /> 193 <param argument="--qRegion" type="text" optional="true" label="Query regions to be considered for interaction prediction" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1"/>
194 </section> 194 </section>
195 <section expanded="True" name="target" title="Target Parameters"> 195 <section expanded="True" name="target" title="Target Parameters">
196 <expand macro="target_macro" /> 196 <expand macro="target_macro"/>
197 <param argument="--tIntLoopMax" help="... to be considered in interactions within the target" label="Maximal number of unpaired bases between neighbored interacting bases" max="30" min="0" type="integer" value="16" /> 197 <param argument="--tIntLoopMax" type="integer" min="0" max="30" value="16" label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the target"/>
198 <param argument="--tRegion" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" label="Target regions to be considered for interaction prediction" optional="true" type="text" /> 198 <param argument="--tRegion" type="text" optional="true" label="Target regions to be considered for interaction prediction" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1"/>
199 </section> 199 </section>
200 <section name="seed" title="Seed Parameters"> 200 <section name="seed" title="Seed Parameters">
201 <expand macro="seed_macro" /> 201 <expand macro="seed_macro"/>
202 <param argument="--seedQMaxUP" help="" label="Max. number of unpaired bases within the query's seed region" max="20" min="-1" type="integer" value="-1" /> 202 <param argument="--seedQMaxUP" type="integer" min="-1" max="20" value="-1" label="Max. number of unpaired bases within the query's seed region" help=""/>
203 <param argument="--seedTMaxUP" help="" label="Max. number of unpaired bases within the target's seed region" max="20" min="-1" type="integer" value="-1" /> 203 <param argument="--seedTMaxUP" type="integer" min="-1" max="20" value="-1" label="Max. number of unpaired bases within the target's seed region" help=""/>
204 <param argument="--seedMaxE" help="" label="Max. energy a seed region may have" max="999" min="-999" type="integer" value="0" /> 204 <param argument="--seedMaxE" type="integer" min="-999" max="999" value="0" label="Max. energy a seed region may have" help=""/>
205 <param argument="--seedMinPu" help="" label="Min. unpaired probability (per sequence)" max="1" min="0" type="float" value="0" /> 205 <param argument="--seedMinPu" type="float" min="0" max="1" value="0" label="Min. unpaired probability (per sequence)" help=""/>
206 <param argument="--seedQRange" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)" label="Interval(s) in the query to search for seeds" optional="true" type="text" value="" /> 206 <param argument="--seedQRange" type="text" value="" optional="true" label="Interval(s) in the query to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
207 <param argument="--seedTRange" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)" label="Interval(s) in the target to search for seeds" optional="true" type="text" value="" /> 207 <param argument="--seedTRange" type="text" value="" optional="true" label="Interval(s) in the target to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
208 </section> 208 </section>
209 <section name="shape" title="SHAPE Input Parameters"> 209 <section name="shape" title="SHAPE Input Parameters">
210 <param argument="--qShape" format="txt" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score" label="SHAPE reactivity data to guide the query's accessibility computation" optional="true" type="data" /> 210 <param argument="--qShape" type="data" format="txt" optional="true" label="SHAPE reactivity data to guide the query's accessibility computation" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score"/>
211 <param argument="--tShape" format="txt" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score" label="SHAPE reactivity data to guide the query's accessibility computation" optional="true" type="data" /> 211 <param argument="--tShape" type="data" format="txt" optional="true" label="SHAPE reactivity data to guide the query's accessibility computation" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score"/>
212 </section> 212 </section>
213 <section name="interaction" title="Prediction Parameters"> 213 <section name="interaction" title="Prediction Parameters">
214 <expand macro="interaction_macro" /> 214 <expand macro="interaction_macro"/>
215 <param argument="--model" help="Sets what to optimize for" label="Prediction target" type="select"> 215 <param argument="--model" type="select" label="Prediction target" help="Sets what to optimize for">
216 <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option> 216 <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option>
217 <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option> 217 <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option>
218 <option value="P">Single-site interaction with minimal free ensemble energy per site</option> 218 <option value="P">Single-site interaction with minimal free ensemble energy per site</option>
219 </param> 219 </param>
220 <param argument="--energyVRNA" help="" label="Energy parameter" type="select"> 220 <param argument="--energyVRNA" type="select" label="Energy parameter" help="">
221 <option value="Turner99">Turner-1999</option> 221 <option value="Turner99">Turner-1999</option>
222 <option selected="true" value="Turner04">Turner-2004</option> 222 <option selected="true" value="Turner04">Turner-2004</option>
223 <option value="Andronescu07">Andronescu-2007</option> 223 <option value="Andronescu07">Andronescu-2007</option>
224 </param> 224 </param>
225 <param argument="--temperature" help="Temperature scaling of ViennaRNA energy parameters" label="Temperature [Celsius]" max="100" min="0" type="integer" value="37" /> 225 <param argument="--temperature" type="integer" min="0" max="100" value="37" label="Temperature [Celsius]" help="Temperature scaling of ViennaRNA energy parameters"/>
226 <param argument="--windowWidth" help="If set, large sequences are decomposed in overlapping windows of the given size to reduce the memory consumption of IntaRNA." label="Window-based computation: window width" max="99999" min="10" optional="True" type="integer" /> 226 <param argument="--windowWidth" type="integer" min="10" max="99999" optional="True" label="Window-based computation: window width" help="If set, large sequences are decomposed in overlapping windows of the given size to reduce the memory consumption of IntaRNA."/>
227 <param argument="--windowOverlap" help="If window width is set, this specifies the overlap of the windows. Note, it has to exceed the maximal interaction length of both query and target." label="Window-based computation: window overlap" max="99999" min="10" type="integer" value="150" /> 227 <param argument="--windowOverlap" type="integer" min="10" max="99999" value="150" label="Window-based computation: window overlap" help="If window width is set, this specifies the overlap of the windows. Note, it has to exceed the maximal interaction length of both query and target."/>
228 </section> 228 </section>
229 <section name="output" title="Output Options"> 229 <section name="output" title="Output Options">
230 <expand macro="output_macro" /> 230 <expand macro="output_macro"/>
231 <param argument="--outMaxE" help="Only interactions with E ≤ maxE are reported" label="Max. absolute energy of an interaction" type="float" value="0" /> 231 <param argument="--outMaxE" type="float" value="0" label="Max. absolute energy of an interaction" help="Only interactions with E ≤ maxE are reported"/>
232 <param argument="--outDeltaE" help="suboptimal output: only interactions with E ≤ (minE+deltaE) are reported" label="Max. delta energy above mfe of an interaction" type="float" value="100" /> 232 <param argument="--outDeltaE" type="float" value="100" label="Max. delta energy above mfe of an interaction" help="suboptimal output: only interactions with E ≤ (minE+deltaE) are reported"/>
233 <conditional name="add_output_cond"> 233 <conditional name="add_output_cond">
234 <param label="Additional output files" name="selector" type="select"> 234 <param name="selector" type="select" label="Additional output files">
235 <option value="add">Output additional files</option> 235 <option value="add">Output additional files</option>
236 <option selected="true" value="none">Don't output additional files</option> 236 <option selected="true" value="none">Don't output additional files</option>
237 </param> 237 </param>
238 <when value="add"> 238 <when value="add">
239 <param display="checkboxes" help="Written in a format similar to RNAplfold unpaired probability output." label="Additional output files" multiple="True" name="add_output" type="select"> 239 <param name="add_output" type="select" label="Additional output files" help="Written in a format similar to RNAplfold unpaired probability output." display="checkboxes" multiple="True">
240 <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option> 240 <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option>
241 <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option> 241 <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option>
242 <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option> 242 <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option>
243 <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option> 243 <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option>
244 <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option> 244 <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option>
247 <option value="tAcc">The target's ED values (tAcc) </option> 247 <option value="tAcc">The target's ED values (tAcc) </option>
248 <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option> 248 <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option>
249 <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option> 249 <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option>
250 </param> 250 </param>
251 </when> 251 </when>
252 <when value="none" /> 252 <when value="none"/>
253 </conditional> 253 </conditional>
254 </section> 254 </section>
255 </when> 255 </when>
256 <when value="basic"> 256 <when value="basic">
257 <section expanded="True" name="query" title="Query Parameters"> 257 <section expanded="True" name="query" title="Query Parameters">
258 <expand macro="query_macro" /> 258 <expand macro="query_macro"/>
259 </section> 259 </section>
260 <section expanded="True" name="target" title="Target Parameters"> 260 <section expanded="True" name="target" title="Target Parameters">
261 <expand macro="target_macro" /> 261 <expand macro="target_macro"/>
262 </section> 262 </section>
263 <section name="seed" title="Seed Parameters"> 263 <section name="seed" title="Seed Parameters">
264 <expand macro="seed_macro" /> 264 <expand macro="seed_macro"/>
265 </section> 265 </section>
266 <section name="interaction" title="Interaction Parameters"> 266 <section name="interaction" title="Interaction Parameters">
267 <expand macro="interaction_macro" /> 267 <expand macro="interaction_macro"/>
268 </section> 268 </section>
269 <section name="output" title="Output Options"> 269 <section name="output" title="Output Options">
270 <expand macro="output_macro" /> 270 <expand macro="output_macro"/>
271 </section> 271 </section>
272 </when> 272 </when>
273 </conditional> 273 </conditional>
274 </inputs> 274 </inputs>
275 <outputs> 275 <outputs>
276 <data format="tabular" label="IntaRNA on ${on_string}" name="outfile" /> 276 <data format="tabular" label="IntaRNA on ${on_string}" name="outfile"/>
277 <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list"> 277 <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list">
278 <filter> 278 <filter>
279 (( 279 ((
280 advancedOptions['advancedSelector'] == "advanced" and 280 advancedOptions['advancedSelector'] == "advanced" and
281 advancedOptions['output']['add_output_cond']['selector'] == "add" and 281 advancedOptions['output']['add_output_cond']['selector'] == "add" and
282 'spotProb' in advancedOptions['output']['add_output_cond']['add_output'] 282 'spotProb' in advancedOptions['output']['add_output_cond']['add_output']
283 )) 283 ))
284 </filter> 284 </filter>
285 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;spotProb.*)\.tabular" visible="true" /> 285 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;spotProb.*)\.tabular" visible="true"/>
286 </collection> 286 </collection>
287 <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list"> 287 <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list">
288 <filter> 288 <filter>
289 (( 289 ((
290 advancedOptions['advancedSelector'] == "advanced" and 290 advancedOptions['advancedSelector'] == "advanced" and
291 advancedOptions['output']['add_output_cond']['selector'] == "add" and 291 advancedOptions['output']['add_output_cond']['selector'] == "add" and
292 'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output'] 292 'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
293 )) 293 ))
294 </filter> 294 </filter>
295 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qSpotProb.*)\.tabular" visible="true" /> 295 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qSpotProb.*)\.tabular" visible="true"/>
296 </collection> 296 </collection>
297 <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list"> 297 <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list">
298 <filter> 298 <filter>
299 (( 299 ((
300 advancedOptions['advancedSelector'] == "advanced" and 300 advancedOptions['advancedSelector'] == "advanced" and
301 advancedOptions['output']['add_output_cond']['selector'] == "add" and 301 advancedOptions['output']['add_output_cond']['selector'] == "add" and
302 'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output'] 302 'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
303 )) 303 ))
304 </filter> 304 </filter>
305 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tSpotProb.*)\.tabular" visible="true" /> 305 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tSpotProb.*)\.tabular" visible="true"/>
306 </collection> 306 </collection>
307 <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list"> 307 <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list">
308 <filter> 308 <filter>
309 (( 309 ((
310 advancedOptions['advancedSelector'] == "advanced" and 310 advancedOptions['advancedSelector'] == "advanced" and
311 advancedOptions['output']['add_output_cond']['selector'] == "add" and 311 advancedOptions['output']['add_output_cond']['selector'] == "add" and
312 'qMinE' in advancedOptions['output']['add_output_cond']['add_output'] 312 'qMinE' in advancedOptions['output']['add_output_cond']['add_output']
313 )) 313 ))
314 </filter> 314 </filter>
315 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qMinE.*)\.tabular" visible="true" /> 315 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qMinE.*)\.tabular" visible="true"/>
316 </collection> 316 </collection>
317 <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list"> 317 <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list">
318 <filter> 318 <filter>
319 (( 319 ((
320 advancedOptions['advancedSelector'] == "advanced" and 320 advancedOptions['advancedSelector'] == "advanced" and
321 advancedOptions['output']['add_output_cond']['selector'] == "add" and 321 advancedOptions['output']['add_output_cond']['selector'] == "add" and
322 'tMinE' in advancedOptions['output']['add_output_cond']['add_output'] 322 'tMinE' in advancedOptions['output']['add_output_cond']['add_output']
323 )) 323 ))
324 </filter> 324 </filter>
325 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tMinE.*)\.tabular" visible="true" /> 325 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tMinE.*)\.tabular" visible="true"/>
326 </collection> 326 </collection>
327 <collection label="For all index combinations: minimal energy of any interaction covering the index pair, on ${on_string}" name="pMinE_output" type="list"> 327 <collection label="For all index combinations: minimal energy of any interaction covering the index pair, on ${on_string}" name="pMinE_output" type="list">
328 <filter> 328 <filter>
329 (( 329 ((
330 advancedOptions['advancedSelector'] == "advanced" and 330 advancedOptions['advancedSelector'] == "advanced" and
331 advancedOptions['output']['add_output_cond']['selector'] == "add" and 331 advancedOptions['output']['add_output_cond']['selector'] == "add" and
332 'pMinE' in advancedOptions['output']['add_output_cond']['add_output'] 332 'pMinE' in advancedOptions['output']['add_output_cond']['add_output']
333 )) 333 ))
334 </filter> 334 </filter>
335 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;pMinE.*)\.tabular" visible="true" /> 335 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;pMinE.*)\.tabular" visible="true"/>
336 </collection> 336 </collection>
337 <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list"> 337 <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list">
338 <filter> 338 <filter>
339 (( 339 ((
340 advancedOptions['advancedSelector'] == "advanced" and 340 advancedOptions['advancedSelector'] == "advanced" and
341 advancedOptions['output']['add_output_cond']['selector'] == "add" and 341 advancedOptions['output']['add_output_cond']['selector'] == "add" and
342 'qAcc' in advancedOptions['output']['add_output_cond']['add_output'] 342 'qAcc' in advancedOptions['output']['add_output_cond']['add_output']
343 )) 343 ))
344 </filter> 344 </filter>
345 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qAcc.*)\.led" visible="true" /> 345 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qAcc.*)\.led" visible="true"/>
346 </collection> 346 </collection>
347 <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list"> 347 <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list">
348 <filter> 348 <filter>
349 (( 349 ((
350 advancedOptions['advancedSelector'] == "advanced" and 350 advancedOptions['advancedSelector'] == "advanced" and
351 advancedOptions['output']['add_output_cond']['selector'] == "add" and 351 advancedOptions['output']['add_output_cond']['selector'] == "add" and
352 'tAcc' in advancedOptions['output']['add_output_cond']['add_output'] 352 'tAcc' in advancedOptions['output']['add_output_cond']['add_output']
353 )) 353 ))
354 </filter> 354 </filter>
355 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\.led" visible="true" /> 355 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\.led" visible="true"/>
356 </collection> 356 </collection>
357 <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list"> 357 <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list">
358 <filter> 358 <filter>
359 (( 359 ((
360 advancedOptions['advancedSelector'] == "advanced" and 360 advancedOptions['advancedSelector'] == "advanced" and
361 advancedOptions['output']['add_output_cond']['selector'] == "add" and 361 advancedOptions['output']['add_output_cond']['selector'] == "add" and
362 'qPu' in advancedOptions['output']['add_output_cond']['add_output'] 362 'qPu' in advancedOptions['output']['add_output_cond']['add_output']
363 )) 363 ))
364 </filter> 364 </filter>
365 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\.lpu" visible="true" /> 365 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\.lpu" visible="true"/>
366 </collection> 366 </collection>
367 <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list"> 367 <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list">
368 <filter> 368 <filter>
369 (( 369 ((
370 advancedOptions['advancedSelector'] == "advanced" and 370 advancedOptions['advancedSelector'] == "advanced" and
371 advancedOptions['output']['add_output_cond']['selector'] == "add" and 371 advancedOptions['output']['add_output_cond']['selector'] == "add" and
372 'tPu' in advancedOptions['output']['add_output_cond']['add_output'] 372 'tPu' in advancedOptions['output']['add_output_cond']['add_output']
373 )) 373 ))
374 </filter> 374 </filter>
375 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\.lpu" visible="true" /> 375 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\.lpu" visible="true"/>
376 </collection> 376 </collection>
377 </outputs> 377 </outputs>
378 <tests> 378 <tests>
379 <test> 379 <test expect_num_outputs="1">
380 <conditional name="advancedOptions"> 380 <conditional name="advancedOptions">
381 <param name="advancedSelector" value="basic" /> 381 <param name="advancedSelector" value="basic"/>
382 <section name="query"> 382 <section name="query">
383 <param name="query" value="intarna_query.fa" /> 383 <param name="query" value="intarna_query.fa"/>
384 </section> 384 </section>
385 <section name="target"> 385 <section name="target">
386 <param name="target" value="intarna_target.fa" /> 386 <param name="target" value="intarna_target.fa"/>
387 </section> 387 </section>
388 </conditional> 388 </conditional>
389 <output file="intarna_result.tabular" name="outfile" /> 389 <output file="intarna_result.tabular" name="outfile"/>
390 </test> 390 </test>
391 <test> 391 <test expect_num_outputs="5">
392 <conditional name="advancedOptions"> 392 <conditional name="advancedOptions">
393 <param name="advancedSelector" value="advanced" /> 393 <param name="advancedSelector" value="advanced"/>
394 <section name="query"> 394 <section name="query">
395 <param name="query" value="intarna_query.fa" /> 395 <param name="query" value="intarna_query.fa"/>
396 </section> 396 </section>
397 <section name="target"> 397 <section name="target">
398 <param name="target" value="intarna_target.fa" /> 398 <param name="target" value="intarna_target.fa"/>
399 </section> 399 </section>
400 <section name="output"> 400 <section name="output">
401 <conditional name="add_output_cond"> 401 <conditional name="add_output_cond">
402 <param name="selector" value="add" /> 402 <param name="selector" value="add"/>
403 <param name="add_output" value="spotProb,qMinE,tAcc,qPu" /> 403 <param name="add_output" value="spotProb,qMinE,tAcc,qPu"/>
404 </conditional> 404 </conditional>
405 </section> 405 </section>
406 </conditional> 406 </conditional>
407 <output file="intarna_result.tabular" name="outfile" /> 407 <output file="intarna_result.tabular" name="outfile"/>
408 <output_collection count="4" name="spotProb_output" type="list"> 408 <output_collection count="4" name="spotProb_output" type="list">
409 </output_collection> 409 </output_collection>
410 <output_collection count="4" name="qMinE_output" type="list"> 410 <output_collection count="4" name="qMinE_output" type="list">
411 </output_collection> 411 </output_collection>
412 <output_collection count="2" name="qPu_output" type="list"> 412 <output_collection count="2" name="qPu_output" type="list">