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comparison intarna.xml @ 7:fd067a1143f3 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
author bgruening
date Mon, 07 Oct 2019 06:18:13 -0400
parents 3f6715821198
children 56f1cef52e96
comparison
equal deleted inserted replaced
6:3f6715821198 7:fd067a1143f3
1 <tool id="intarna" name="IntaRNA" version="2.2.0"> 1 <tool id="intarna" name="IntaRNA" version="3.1.1">
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 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" /> 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" />
6 <conditional name="qAcc_cond"> 6 <conditional name="qAcc_cond">
7 <param argument="--qAcc" type="select" label="Accessibility computation" help=""> 7 <param argument="--qAcc" help="" label="Accessibility computation" type="select">
8 <option value="N">No accessibility contributions ('N')</option> 8 <option value="N">No accessibility contributions ('N')</option>
9 <option value="C" selected="true">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" type="data" label="Accessibility computation" help="" /> 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" />
17 </when> 17 </when>
18 <when value="E"> 18 <when value="E">
19 <param argument="--qAccFile" format="txt" type="data" label="Accessibility computation" help="" /> 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" />
20 </when> 20 </when>
21 </conditional> 21 </conditional>
22 <param argument="--qAccW" type="integer" value="150" min="0" max="99999" 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" />
23 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" />
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> 24 </macro>
27 <macro name="target_macro"> 25 <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" /> 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" />
29 <conditional name="tAcc_cond"> 27 <conditional name="tAcc_cond">
30 <param argument="--tAcc" type="select" label="Accessibility computation" help=""> 28 <param argument="--tAcc" help="" label="Accessibility computation" type="select">
31 <option value="N">No accessibility contributions ('N')</option> 29 <option value="N">No accessibility contributions ('N')</option>
32 <option value="C" selected="true">Computation of accessibilities ('C')</option> 30 <option selected="true" value="C">Computation of accessibilities ('C')</option>
33 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option> 31 <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> 32 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
35 </param> 33 </param>
36 <when value="N"/> 34 <when value="N" />
37 <when value="C"/> 35 <when value="C" />
38 <when value="P"> 36 <when value="P">
39 <param argument="--tAccFile" format="txt" type="data" label="The file to be parsed" help="... for accessibility computation" /> 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" />
40 </when> 38 </when>
41 <when value="E"> 39 <when value="E">
42 <param argument="--tAccFile" format="txt" type="data" label="Accessibility computation" help="" /> 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" />
43 </when> 41 </when>
44 </conditional> 42 </conditional>
45 <param argument="--tAccW" type="integer" value="150" min="0" max="99999" 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" />
46 label="Max. interaction length" help="... for query 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" />
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> 45 </macro>
50 <macro name="seed_macro"> 46 <macro name="seed_macro">
51 <param argument="--noSeed" truevalue="--noSeed" falsevalue="" checked="false" type="boolean" 47 <param argument="--noSeed" checked="false" falsevalue="" help="" label="Disable seed constraint entirely for computation" truevalue="--noSeed" type="boolean" />
52 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" />
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"/> 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" />
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> 50 </macro>
57 <macro name="interaction_macro"> 51 <macro name="interaction_macro">
58 <param argument="--mode" type="select" label="Prediction mode" help=""> 52 <param argument="--mode" help="" label="Prediction mode" type="select">
59 <option value="H" selected="true">Heuristic (fast and low memory)</option> 53 <option selected="true" value="H">Heuristic ('H')</option>
60 <option value="M">Exact and low memory</option> 54 <option value="M">Exact but slow ('M')</option>
61 <option value="E">Exact (high memory)</option>
62 </param> 55 </param>
63 </macro> 56 </macro>
64 <macro name="output_macro"> 57 <macro name="output_macro">
65 <param argument="--outMode" type="select" label="Output Mode" help=""> 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" />
66 <option value="N">Normal output (ASCII char + energy)</option> 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" />
67 <option value="D">Detailed output (ASCII char + energy/position details)</option> 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" />
68 <option value="C" selected="true">CSV output (see --outCsvCols)</option> 61 <param argument="--outOverlap" help="Whether or not interactions can overlap" label="Overlapping of suboptimal predictions" type="select">
69 <option value="1">backward compatible IntaRNA v1.* normal output</option> 62 <option value="N">in none of the sequences</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> 63 <option value="T">in the target only</option>
81 <option value="Q" selected="true">in the query only</option> 64 <option selected="true" value="Q">in the query only</option>
82 <option value="B">in both sequences</option> 65 <option value="B">in both sequences</option>
83 </param> 66 </param>
84 </macro> 67 </macro>
85 </macros> 68 </macros>
86 <requirements> 69 <requirements>
87 <requirement type="package" version="2.2.0">intarna</requirement> 70 <requirement type="package" version="3.1.1">intarna</requirement>
88 </requirements> 71 </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> 72 <version_command>IntaRNA --version</version_command>
94 <command> 73 <command detect_errors="exit_code"><![CDATA[
95 <![CDATA[ 74
96 IntaRNA 75 IntaRNA
97 #if $advancedOptions.advancedSelector == "advanced" 76 #if $advancedOptions.advancedSelector == "advanced"
98 ## Query parameters 77 ## Query parameters
99 --query '$advancedOptions.query._query' 78 --query '$advancedOptions.query.query'
100 --qAcc $advancedOptions.query.qAcc_cond.qAcc 79 --qAcc $advancedOptions.query.qAcc_cond.qAcc
101 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E" 80 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
102 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile' 81 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
103 #end if 82 #end if
104 --qAccW $advancedOptions.query.qAccW 83 --qAccW $advancedOptions.query.qAccW
105 --qAccL $advancedOptions.query.qAccL 84 --qAccL $advancedOptions.query.qAccL
106 ## #if $advancedOptions.query.qAccConstr <> "."
107 ## --qAccConstr $advancedOptions.query.qAccConstr
108 ## #end if
109 --qIntLoopMax $advancedOptions.query.qIntLoopMax 85 --qIntLoopMax $advancedOptions.query.qIntLoopMax
110 #if $advancedOptions.query.qRegion 86 #if $advancedOptions.query.qRegion
111 --qRegion '$advancedOptions.query.qRegion' 87 --qRegion '$advancedOptions.query.qRegion'
112 #end if 88 #end if
113
114 ## Target param. 89 ## Target param.
115 --target '$advancedOptions.target._target' 90 --target '$advancedOptions.target.target'
116 --tAcc $advancedOptions.target.tAcc_cond.tAcc 91 --tAcc $advancedOptions.target.tAcc_cond.tAcc
117 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E" 92 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
118 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile' 93 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
119 #end if 94 #end if
120 --tAccW $advancedOptions.target.tAccW 95 --tAccW $advancedOptions.target.tAccW
121 --tAccL $advancedOptions.target.tAccL 96 --tAccL $advancedOptions.target.tAccL
122 ## #if $advancedOptions.target.tAccConstr <> "."
123 ## --tAccConstr $advancedOptions.target.tAccConstr
124 ## #end if
125 --tIntLoopMax $advancedOptions.target.tIntLoopMax 97 --tIntLoopMax $advancedOptions.target.tIntLoopMax
126 #if $advancedOptions.target.tRegion 98 #if $advancedOptions.target.tRegion
127 --tRegion '$advancedOptions.target.tRegion' 99 --tRegion '$advancedOptions.target.tRegion'
128 #end if 100 #end if
129
130 ## Seed param. 101 ## Seed param.
131 $advancedOptions.seed.noSeed 102 #if $advancedOptions.seed.noSeed
132 --seedBP $advancedOptions.seed.seedBP 103 $advancedOptions.seed.noSeed
133 --seedMaxUP $advancedOptions.seed.seedMaxUP 104 #else
134 --seedQMaxUP $advancedOptions.seed.seedQMaxUP 105 --seedBP $advancedOptions.seed.seedBP
135 --seedTMaxUP $advancedOptions.seed.seedTMaxUP 106 --seedMaxE $advancedOptions.seed.seedMaxE
136 --seedMaxE $advancedOptions.seed.seedMaxE 107 --seedMinPu $advancedOptions.seed.seedMinPu
137 --seedMinPu $advancedOptions.seed.seedMinPu 108 #if $advancedOptions.seed.seedMaxUP > 0
138 --seedQRange '$advancedOptions.seed.seedQRange' 109 --seedMaxUP $advancedOptions.seed.seedMaxUP
139 --seedTRange '$advancedOptions.seed.seedTRange' 110 #end if
140 111 #if $advancedOptions.seed.seedQMaxUP
141 ## Interaction param. 112 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
113 #end if
114 #if $advancedOptions.seed.seedTMaxUP
115 --seedTMaxUP $advancedOptions.seed.seedTMaxUP
116 #end if
117 #if $advancedOptions.seed.seedQRange
118 --seedQRange '$advancedOptions.seed.seedQRange'
119 #end if
120 #if $advancedOptions.seed.seedTRange
121 --seedTRange '$advancedOptions.seed.seedTRange'
122 #end if
123 #end if
124 ## SHAPE param.
125 #if $advancedOptions.shape.qShape
126 --qShape '$advancedOptions.shape.qShape'
127 #end if
128 #if $advancedOptions.shape.tShape
129 --tShape '$advancedOptions.shape.tShape'
130 #end if
131 ## Prediction param.
142 --mode $advancedOptions.interaction.mode 132 --mode $advancedOptions.interaction.mode
143 --pred $advancedOptions.interaction.pred 133 --model $advancedOptions.interaction.model
144 --energy $advancedOptions.interaction.energy 134 --energy V
145 #if $advancedOptions.interaction.energyVRNA 135 --energyVRNA '$advancedOptions.interaction.energyVRNA'
146 --energyVRNA '$advancedOptions.interaction.energyVRNA'
147 #end if
148 --temperature $advancedOptions.interaction.temperature 136 --temperature $advancedOptions.interaction.temperature
149 137 #if $advancedOptions.interaction.windowWidth
138 --windowWidth $advancedOptions.interaction.windowWidth
139 --windowOverlap $advancedOptions.interaction.windowOverlap
140 #end if
141
150 ##Output param. 142 ##Output param.
151 --out ./temp_tabular_output 143 ## create temporary output file to be converted to tab-separated output (see below)
152 --outMode $advancedOptions.output.outMode 144 --out STDOUT
145 --outMode C
146 --outCsvCols '$advancedOptions.output.outCsvCols'
147 --outCsvSort '$advancedOptions.output.outCsvSort'
153 --outNumber $advancedOptions.output.outNumber 148 --outNumber $advancedOptions.output.outNumber
154 --outOverlap $advancedOptions.output.outOverlap 149 --outOverlap $advancedOptions.output.outOverlap
155 --outMaxE $advancedOptions.output.outMaxE 150 --outMaxE $advancedOptions.output.outMaxE
156 --outDeltaE $advancedOptions.output.outDeltaE 151 --outDeltaE $advancedOptions.output.outDeltaE
157 #if $advancedOptions.output.outCsvCols 152 ## add additional output files
158 --outCsvCols '$advancedOptions.output.outCsvCols'
159 #end if
160 #if $advancedOptions.output.add_output_cond.selector == "add" 153 #if $advancedOptions.output.add_output_cond.selector == "add"
161 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None' 154 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
162 #for j in $advancedOptions.output.add_output_cond.add_output.value: 155 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
163 --$j $getVar($j) 156 #if $outFile == 'qAcc' or $outFile == 'tAcc'
164 #end for 157 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.led'
165 #end if 158 #else
166 #end if 159 #if $outFile == 'qAcc' or $outFile == 'tAcc' or $outFile == 'qPu' or $outFile == 'tPu'
167 160 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.lpu'
161 #else
162 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.tabular'
163 #end if
164 #end if
165 --out '$curOutFile'
166 #end for
167 #end if
168 #end if
168 #elif $advancedOptions.advancedSelector == "basic" 169 #elif $advancedOptions.advancedSelector == "basic"
169 ## Query parameters 170 ## Query parameters
170 --query '$advancedOptions.query._query' 171 --query '$advancedOptions.query.query'
171 --qAcc $advancedOptions.query.qAcc_cond.qAcc 172 --qAcc $advancedOptions.query.qAcc_cond.qAcc
172 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E" 173 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
173 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile' 174 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
174 #end if 175 #end if
175 --qAccW $advancedOptions.query.qAccW 176 --qAccW $advancedOptions.query.qAccW
176 --qAccL $advancedOptions.query.qAccL 177 --qAccL $advancedOptions.query.qAccL
177
178 ## Target param. 178 ## Target param.
179 --target '$advancedOptions.target._target' 179 --target '$advancedOptions.target.target'
180 --tAcc $advancedOptions.target.tAcc_cond.tAcc 180 --tAcc $advancedOptions.target.tAcc_cond.tAcc
181 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E" 181 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
182 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile' 182 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
183 #end if 183 #end if
184 --tAccW $advancedOptions.target.tAccW 184 --tAccW $advancedOptions.target.tAccW
185 --tAccL $advancedOptions.target.tAccL 185 --tAccL $advancedOptions.target.tAccL
186
187 ## Seed param. 186 ## Seed param.
188 $advancedOptions.seed.noSeed 187 #if $advancedOptions.seed.noSeed
189 --seedBP $advancedOptions.seed.seedBP 188 $advancedOptions.seed.noSeed
190 --seedMaxUP $advancedOptions.seed.seedMaxUP 189 #else
191 190 --seedBP $advancedOptions.seed.seedBP
192 ## Interaction param. 191 --seedMaxUP $advancedOptions.seed.seedMaxUP
192 #end if
193 ## Prediction param.
193 --mode $advancedOptions.interaction.mode 194 --mode $advancedOptions.interaction.mode
194 195 ## Output param.
195 ##Output param. 196 ## create temporary output file to be converted to tab-separated output (see below)
196 --out ./temp_tabular_output 197 --out STDOUT
197 --outMode $advancedOptions.output.outMode
198 --outNumber $advancedOptions.output.outNumber 198 --outNumber $advancedOptions.output.outNumber
199 --outOverlap $advancedOptions.output.outOverlap 199 --outOverlap $advancedOptions.output.outOverlap
200 #if $advancedOptions.output.outCsvCols 200 --outMode C
201 --outCsvCols '$advancedOptions.output.outCsvCols' 201 --outCsvCols '$advancedOptions.output.outCsvCols'
202 #end if 202 --outCsvSort '$advancedOptions.output.outCsvSort'
203 #end if 203 #end if
204 && sed 's/\t/ /g' ./temp_tabular_output > ./temp_output_no_tabs 204
205 && sed 's/;/\t/g' ./temp_output_no_tabs > '$outfile' 205 ## Multithreading param.
206 206 --threads "\${GALAXY_SLOTS:-1}"
207 ]]> 207 ## convert semicolon-separated output to tab-separated file
208 | sed 's/\t/ /g' | sed 's/;/\t/g' > '$outfile'
209 ## convert additional semicolon-separated output to tab-separated file
210 #if $advancedOptions.advancedSelector == "advanced"
211 #if $advancedOptions.output.add_output_cond.selector == "add"
212 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
213 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
214 #if $outFile != 'qAcc' and $outFile != 'tAcc' and $outFile != 'qPu' and $outFile != 'tPu'
215 #set curOutFile = 'intarna_' + str($outFile) + '*.tabular'
216 && sed -i 's/\t/ /g' $curOutFile
217 && sed -i 's/;/\t/g' $curOutFile
218 #end if
219 #end for
220 #end if
221 #end if
222 #end if
223 ]]>
208 </command> 224 </command>
209 <inputs> 225 <inputs>
210
211 <conditional name="advancedOptions"> 226 <conditional name="advancedOptions">
212 <param name="advancedSelector" type="select" label="Options"> 227 <param label="Options" name="advancedSelector" type="select">
213 <option value="basic">Basic Options</option> 228 <option value="basic">Basic Options</option>
214 <option value="advanced">Advanced Options</option> 229 <option value="advanced">Advanced Options</option>
215 </param> 230 </param>
216 <when value="advanced"> 231 <when value="advanced">
217 <section name="query" title="Query Parameters" expanded="True"> 232 <section expanded="True" name="query" title="Query Parameters">
218 <expand macro="query_macro"/> 233 <expand macro="query_macro" />
219 <!-- 234 <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" />
220 <param name="qAccConstr" type="select" label="Structure constraint for each sequence position" help=""> 235 <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" />
221 <option value="." selected="true">No constraint</option> 236 </section>
222 <option value="x">Unpaired</option> 237 <section expanded="True" name="target" title="Target Parameters">
223 <option value="b">Blocked positions are excluded from interaction prediction and considered unpaired </option> 238 <expand macro="target_macro" />
239 <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" />
240 <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" />
241 </section>
242 <section name="seed" title="Seed Parameters">
243 <expand macro="seed_macro" />
244 <param argument="--seedQMaxUP" help="" label="Max. number of unpaired bases within the query's seed region" max="20" min="-1" type="integer" value="-1" />
245 <param argument="--seedTMaxUP" help="" label="Max. number of unpaired bases within the target's seed region" max="20" min="-1" type="integer" value="-1" />
246 <param argument="--seedMaxE" help="" label="Max. energy a seed region may have" max="999" min="-999" type="integer" value="0" />
247 <param argument="--seedMinPu" help="" label="Min. unpaired probability (per sequence)" max="1" min="0" type="float" value="0" />
248 <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="" />
249 <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="" />
250 </section>
251 <section name="shape" title="SHAPE Input Parameters">
252 <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" />
253 <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" />
254 </section>
255 <section name="interaction" title="Prediction Parameters">
256 <expand macro="interaction_macro" />
257 <param argument="--model" help="Sets what to optimize for" label="Prediction target" type="select">
258 <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option>
259 <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option>
260 <option value="P">Single-site interaction with minimal free ensemble energy per site</option>
224 </param> 261 </param>
225 --> 262 <param argument="--energyVRNA" help="" label="Energy parameter" type="select">
226 <param argument="--qIntLoopMax" type="integer" value="16" min="0" max="30" 263 <option value="Turner99">Turner-1999</option>
227 label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the query"/> 264 <option selected="true" value="Turner04">Turner-2004</option>
228 <param argument="--qRegion" type="text" optional="true" label="Query regions to be considered for interaction prediction" 265 <option value="Andronescu07">Andronescu-2007</option>
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> 266 </param>
238 --> 267 <param argument="--temperature" help="Temperature scaling of ViennaRNA energy parameters" label="Temperature [Celsius]" max="100" min="0" type="integer" value="37" />
239 268 <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" />
240 <param argument="--tIntLoopMax" type="integer" value="16" min="0" max="30" 269 <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" />
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="txt" 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> 270 </section>
276 <section name="output" title="Output Options"> 271 <section name="output" title="Output Options">
277 <expand macro="output_macro"/> 272 <expand macro="output_macro" />
278 <param argument="--outMaxE" type="float" value="0" 273 <param argument="--outMaxE" help="Only interactions with E ≤ maxE are reported" label="Max. absolute energy of an interaction" type="float" value="0" />
279 label="Max. absolute energy of an interaction" help="Only interactions with E &#8804; maxE are reported"/> 274 <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" />
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"> 275 <conditional name="add_output_cond">
284 <param name="selector" type="select" label="Additional output files"> 276 <param label="Additional output files" name="selector" type="select">
285 <option value="add">Output additional files</option> 277 <option value="add">Output additional files</option>
286 <option value="none" selected="true">Don't output additional files</option> 278 <option selected="true" value="none">Don't output additional files</option>
287 </param> 279 </param>
288 <when value="add"> 280 <when value="add">
289 <param name="add_output" type="select" display="checkboxes" multiple="True" 281 <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">
290 label="Additional output files" help="Written in a format similar to RNAplfold unpaired probability output."> 282 <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option>
291 <option value="outQAccFile" selected="true">The query's ED values (--outQAccFile)</option> 283 <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option>
292 <option value="outTAccFile">The target's ED values (--outTAccFile) </option> 284 <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option>
293 <option value="outQPuFile">The query's unpaired probabilities used for ED values (--outQPuFile) </option> 285 <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option>
294 <option value="outTPuFile">The target's unpaired probabilities used for ED values (--outTPuFile)</option> 286 <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option>
287 <option value="tMinE">For all target indices: minimal energy of any interaction covering the position (tMinE)</option>
288 <option value="qAcc">The query's ED values (qAcc)</option>
289 <option value="tAcc">The target's ED values (tAcc) </option>
290 <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option>
291 <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option>
295 </param> 292 </param>
296 </when> 293 </when>
297 <when value="none"/> 294 <when value="none" />
298 </conditional> 295 </conditional>
299
300 </section> 296 </section>
301 </when> 297 </when>
302 <when value="basic"> 298 <when value="basic">
303 <section name="query" title="Query Parameters" expanded="True"> 299 <section expanded="True" name="query" title="Query Parameters">
304 <expand macro="query_macro"/> 300 <expand macro="query_macro" />
305 </section> 301 </section>
306 <section name="target" title="Target Parameters" expanded="True"> 302 <section expanded="True" name="target" title="Target Parameters">
307 <expand macro="target_macro"/> 303 <expand macro="target_macro" />
308 </section> 304 </section>
309 <section name="seed" title="Seed Parameters"> 305 <section name="seed" title="Seed Parameters">
310 <expand macro="seed_macro"/> 306 <expand macro="seed_macro" />
311 </section> 307 </section>
312 <section name="interaction" title="Interaction Parameters"> 308 <section name="interaction" title="Interaction Parameters">
313 <expand macro="interaction_macro"/> 309 <expand macro="interaction_macro" />
314 </section> 310 </section>
315 <section name="output" title="Output Options"> 311 <section name="output" title="Output Options">
316 <expand macro="output_macro"/> 312 <expand macro="output_macro" />
317 </section> 313 </section>
318 </when> 314 </when>
319 </conditional> 315 </conditional>
320 </inputs> 316 </inputs>
321 <outputs> 317 <outputs>
322 <data name="outfile" format="txt" label="IntaRNA on ${on_string}"> 318 <data format="tabular" label="IntaRNA on ${on_string}" name="outfile" />
323 <change_format> 319 <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list">
324 <when input="advancedOptions.output.outMode" value="C" format="tabular" /> 320 <filter>
325 </change_format> 321 ((
326 </data> 322 advancedOptions['advancedSelector'] == "advanced" and
327 <data name="outQAccFile" format="txt" label="Query's ED values, on ${on_string}"> 323 advancedOptions['output']['add_output_cond']['selector'] == "add" and
328 <filter> 324 'spotProb' in advancedOptions['output']['add_output_cond']['add_output']
329 (( 325 ))
330 advancedOptions['advancedSelector'] == "advanced" and 326 </filter>
331 advancedOptions['output']['add_output_cond']['selector'] == "add" and 327 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;spotProb.*)\.tabular" visible="true" />
332 'outQAccFile' in advancedOptions['output']['add_output_cond']['add_output'] 328 </collection>
333 )) 329 <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list">
334 </filter> 330 <filter>
335 </data> 331 ((
336 <data name="outTAccFile" format="txt" label="Target's ED values, on ${on_string}"> 332 advancedOptions['advancedSelector'] == "advanced" and
337 <filter> 333 advancedOptions['output']['add_output_cond']['selector'] == "add" and
338 (( 334 'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
339 advancedOptions['advancedSelector'] == "advanced" and 335 ))
340 advancedOptions['output']['add_output_cond']['selector'] == "add" and 336 </filter>
341 'outTAccFile' in advancedOptions['output']['add_output_cond']['add_output'] 337 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qSpotProb.*)\.tabular" visible="true" />
342 )) 338 </collection>
343 </filter> 339 <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list">
344 </data> 340 <filter>
345 <data name="outQPuFile" format="txt" label="Query's unpaired probabilities used for ED values, on ${on_string}"> 341 ((
346 <filter> 342 advancedOptions['advancedSelector'] == "advanced" and
347 (( 343 advancedOptions['output']['add_output_cond']['selector'] == "add" and
348 advancedOptions['advancedSelector'] == "advanced" and 344 'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
349 advancedOptions['output']['add_output_cond']['selector'] == "add" and 345 ))
350 'outQPuFile' in advancedOptions['output']['add_output_cond']['add_output'] 346 </filter>
351 )) 347 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tSpotProb.*)\.tabular" visible="true" />
352 </filter> 348 </collection>
353 </data> 349 <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list">
354 <data name="outTPuFile" format="txt" label="Target's unpaired probabilities used for ED values, on ${on_string}"> 350 <filter>
355 <filter> 351 ((
356 (( 352 advancedOptions['advancedSelector'] == "advanced" and
357 advancedOptions['advancedSelector'] == "advanced" and 353 advancedOptions['output']['add_output_cond']['selector'] == "add" and
358 advancedOptions['output']['add_output_cond']['selector'] == "add" and 354 'qMinE' in advancedOptions['output']['add_output_cond']['add_output']
359 'outTPuFile' in advancedOptions['output']['add_output_cond']['add_output'] 355 ))
360 )) 356 </filter>
361 </filter> 357 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qMinE.*)\.tabular" visible="true" />
362 </data> 358 </collection>
359 <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list">
360 <filter>
361 ((
362 advancedOptions['advancedSelector'] == "advanced" and
363 advancedOptions['output']['add_output_cond']['selector'] == "add" and
364 'tMinE' in advancedOptions['output']['add_output_cond']['add_output']
365 ))
366 </filter>
367 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tMinE.*)\.tabular" visible="true" />
368 </collection>
369 <collection label="For all index combinations: minimal energy of any interaction covering the index pair, on ${on_string}" name="pMinE_output" type="list">
370 <filter>
371 ((
372 advancedOptions['advancedSelector'] == "advanced" and
373 advancedOptions['output']['add_output_cond']['selector'] == "add" and
374 'pMinE' in advancedOptions['output']['add_output_cond']['add_output']
375 ))
376 </filter>
377 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;pMinE.*)\.tabular" visible="true" />
378 </collection>
379 <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list">
380 <filter>
381 ((
382 advancedOptions['advancedSelector'] == "advanced" and
383 advancedOptions['output']['add_output_cond']['selector'] == "add" and
384 'qAcc' in advancedOptions['output']['add_output_cond']['add_output']
385 ))
386 </filter>
387 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qAcc.*)\.led" visible="true" />
388 </collection>
389 <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list">
390 <filter>
391 ((
392 advancedOptions['advancedSelector'] == "advanced" and
393 advancedOptions['output']['add_output_cond']['selector'] == "add" and
394 'tAcc' in advancedOptions['output']['add_output_cond']['add_output']
395 ))
396 </filter>
397 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\.led" visible="true" />
398 </collection>
399 <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list">
400 <filter>
401 ((
402 advancedOptions['advancedSelector'] == "advanced" and
403 advancedOptions['output']['add_output_cond']['selector'] == "add" and
404 'qPu' in advancedOptions['output']['add_output_cond']['add_output']
405 ))
406 </filter>
407 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\.lpu" visible="true" />
408 </collection>
409 <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list">
410 <filter>
411 ((
412 advancedOptions['advancedSelector'] == "advanced" and
413 advancedOptions['output']['add_output_cond']['selector'] == "add" and
414 'tPu' in advancedOptions['output']['add_output_cond']['add_output']
415 ))
416 </filter>
417 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\.lpu" visible="true" />
418 </collection>
363 </outputs> 419 </outputs>
364 <tests> 420 <tests>
365 <test> 421 <test>
366 <conditional name="advancedOptions"> 422 <conditional name="advancedOptions">
367 <param name="advancedSelector" value="basic"/> 423 <param name="advancedSelector" value="basic" />
368 <section name="query"> 424 <section name="query">
369 <param name="_query" value="intarna_query.fa" /> 425 <param name="query" value="intarna_query.fa" />
370 </section> 426 </section>
371 <section name="target"> 427 <section name="target">
372 <param name="_target" value="intarna_target.fa"/> 428 <param name="target" value="intarna_target.fa" />
373 </section> 429 </section>
374 </conditional> 430 </conditional>
375 <output name="outfile" file="intarna_result.tabular"/> 431 <output file="intarna_result.tabular" name="outfile" />
432 </test>
433 <test>
434 <conditional name="advancedOptions">
435 <param name="advancedSelector" value="advanced" />
436 <section name="query">
437 <param name="query" value="intarna_query.fa" />
438 </section>
439 <section name="target">
440 <param name="target" value="intarna_target.fa" />
441 </section>
442 <section name="output">
443 <conditional name="add_output_cond">
444 <param name="selector" value="add" />
445 <param name="add_output" value="spotProb,qMinE,tAcc,qPu" />
446 </conditional>
447 </section>
448 </conditional>
449 <output file="intarna_result.tabular" name="outfile" />
450 <output_collection count="4" name="spotProb_output" type="list">
451 </output_collection>
452 <output_collection count="4" name="qMinE_output" type="list">
453 </output_collection>
454 <output_collection count="2" name="qPu_output" type="list">
455 </output_collection>
456 <output_collection count="2" name="tAcc_output" type="list">
457 </output_collection>
376 </test> 458 </test>
377 </tests> 459 </tests>
378 460 <help><![CDATA[
379 <help>
380 <![CDATA[
381 461
382 **What it does** 462 **What it does**
383
384 Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites 463 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. 464 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. 465 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 466 .. class:: infomark
391
392 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information. 467 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information.
393
394
395 **Input** 468 **Input**
396
397
398
399 RNA sequences in *FASTA* format 469 RNA sequences in *FASTA* format
400
401
402 **Output** 470 **Output**
403
404 RNA-RNA interaction information in CSV format and additional information/files on demand 471 RNA-RNA interaction information in CSV format and additional information/files on demand
405 472
406 ]]> 473 ]]>
407
408 </help> 474 </help>
409
410 <citations> 475 <citations>
411 <citation type="doi">10.1093/nar/gkx279</citation> 476 <citation type="doi">10.1093/nar/gkx279</citation>
412 <citation type="doi">10.1093/nar/gku359</citation> 477 <citation type="doi">10.1093/nar/gku359</citation>
413 <citation type="doi">10.1093/bioinformatics/btn544</citation> 478 <citation type="doi">10.1093/bioinformatics/btn544</citation>
414 </citations> 479 </citations>
415
416 </tool> 480 </tool>