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annotate intarna.xml @ 13:ddfd02440cfa draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 76e8f82fd859dcb91b5704df4fd5d2d154ad799e"
author bgruening
date Tue, 12 Apr 2022 15:47:18 +0000
parents 0a2817800fd9
children d3db19200b24
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13
ddfd02440cfa "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 76e8f82fd859dcb91b5704df4fd5d2d154ad799e"
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1 <tool id="intarna" name="IntaRNA" version="3.3.1">
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33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
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3 <macros>
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4 <macro name="query_macro">
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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" />
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6 <conditional name="qAcc_cond">
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fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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7 <param argument="--qAcc" help="" label="Accessibility computation" type="select">
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8 <option value="N">No accessibility contributions ('N')</option>
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9 <option selected="true" value="C">Computation of accessibilities ('C')</option>
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10 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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11 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
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12 </param>
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13 <when value="N" />
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14 <when value="C" />
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15 <when value="P">
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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" />
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17 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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18 <when value="E">
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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" />
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20 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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21 </conditional>
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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" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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24 </macro>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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25 <macro name="target_macro">
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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" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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27 <conditional name="tAcc_cond">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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28 <param argument="--tAcc" help="" label="Accessibility computation" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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29 <option value="N">No accessibility contributions ('N')</option>
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30 <option selected="true" value="C">Computation of accessibilities ('C')</option>
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31 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
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32 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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33 </param>
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34 <when value="N" />
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35 <when value="C" />
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36 <when value="P">
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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" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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38 </when>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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39 <when value="E">
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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" />
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41 </when>
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42 </conditional>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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" />
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45 </macro>
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46 <macro name="seed_macro">
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47 <param argument="--noSeed" checked="false" falsevalue="" help="" label="Disable seed constraint entirely for computation" truevalue="--noSeed" type="boolean" />
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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" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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" />
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50 </macro>
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51 <macro name="interaction_macro">
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52 <param argument="--mode" help="" label="Prediction mode" type="select">
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53 <option selected="true" value="H">Heuristic ('H')</option>
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54 <option value="M">Exact but slow ('M')</option>
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55 </param>
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56 </macro>
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57 <macro name="output_macro">
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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" />
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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" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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61 <param argument="--outOverlap" help="Whether or not interactions can overlap" label="Overlapping of suboptimal predictions" type="select">
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62 <option value="N">in none of the sequences</option>
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63 <option value="T">in the target only</option>
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64 <option selected="true" value="Q">in the query only</option>
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65 <option value="B">in both sequences</option>
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66 </param>
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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" />
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68 </macro>
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69 </macros>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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70 <requirements>
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71 <requirement type="package" version="3.3.1">intarna</requirement>
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72 </requirements>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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73 <version_command>IntaRNA --version</version_command>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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74 <command detect_errors="exit_code"><![CDATA[
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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75
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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76 IntaRNA
9
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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77 ## Multithreading
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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78 --threads "\${GALAXY_SLOTS:-1}"
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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79 ## basic general parameters
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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80 ## Query parameters
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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81 --query '$advancedOptions.query.query'
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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82 --qAcc $advancedOptions.query.qAcc_cond.qAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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83 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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84 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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85 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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diff changeset
86 --qAccW $advancedOptions.query.qAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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87 --qAccL $advancedOptions.query.qAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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88 ## Target param.
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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89 --target '$advancedOptions.target.target'
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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90 --tAcc $advancedOptions.target.tAcc_cond.tAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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91 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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92 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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93 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
94 --tAccW $advancedOptions.target.tAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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95 --tAccL $advancedOptions.target.tAccL
9
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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96 ## Seed param.
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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97 #if $advancedOptions.seed.noSeed
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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98 $advancedOptions.seed.noSeed
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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99 #else
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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100 --seedBP $advancedOptions.seed.seedBP
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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101 #if $advancedOptions.seed.seedMaxUP > 0
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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102 --seedMaxUP $advancedOptions.seed.seedMaxUP
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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103 #end if
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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104 #end if
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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105 ## Prediction param.
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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106 --mode $advancedOptions.interaction.mode
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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107 --energy V
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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108 ## Output param.
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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109 --out $outfile
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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110 --outMode C
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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111 --outSep "`printf "\t"`"
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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112 --outNumber $advancedOptions.output.outNumber
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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113 --outOverlap $advancedOptions.output.outOverlap
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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114 --outCsvCols '$advancedOptions.output.outCsvCols'
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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115 --outCsvSort '$advancedOptions.output.outCsvSort'
13
ddfd02440cfa "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 76e8f82fd859dcb91b5704df4fd5d2d154ad799e"
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116 $advancedOptions.output.outPairwise
9
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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117 #if $advancedOptions.advancedSelector == "advanced"
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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118 ## Query parameters
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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119 --qIntLoopMax $advancedOptions.query.qIntLoopMax
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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120 #if $advancedOptions.query.qRegion
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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121 --qRegion '$advancedOptions.query.qRegion'
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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122 #end if
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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123 ## Target param.
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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124 --tIntLoopMax $advancedOptions.target.tIntLoopMax
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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125 #if $advancedOptions.target.tRegion
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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126 --tRegion '$advancedOptions.target.tRegion'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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127 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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128 ## Seed param.
9
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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129 #if not $advancedOptions.seed.noSeed
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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130 --seedMaxE $advancedOptions.seed.seedMaxE
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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131 --seedMinPu $advancedOptions.seed.seedMinPu
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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132 #if $advancedOptions.seed.seedQMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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133 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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134 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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135 #if $advancedOptions.seed.seedTMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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136 --seedTMaxUP $advancedOptions.seed.seedTMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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137 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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138 #if $advancedOptions.seed.seedQRange
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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139 --seedQRange '$advancedOptions.seed.seedQRange'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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140 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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141 #if $advancedOptions.seed.seedTRange
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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142 --seedTRange '$advancedOptions.seed.seedTRange'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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143 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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144 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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145 ## SHAPE param.
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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146 #if $advancedOptions.shape.qShape
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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147 --qShape '$advancedOptions.shape.qShape'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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148 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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149 #if $advancedOptions.shape.tShape
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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150 --tShape '$advancedOptions.shape.tShape'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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151 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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152 ## Prediction param.
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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153 --model $advancedOptions.interaction.model
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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154 --energyVRNA '$advancedOptions.interaction.energyVRNA'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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155 --temperature $advancedOptions.interaction.temperature
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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156 #if $advancedOptions.interaction.windowWidth
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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157 --windowWidth $advancedOptions.interaction.windowWidth
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158 --windowOverlap $advancedOptions.interaction.windowOverlap
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159 #end if
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160 ##Output param.
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161 --outMaxE $advancedOptions.output.outMaxE
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162 --outDeltaE $advancedOptions.output.outDeltaE
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163 ## add additional output files
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164 #if $advancedOptions.output.add_output_cond.selector == "add"
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165 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
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166 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
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167 #if $outFile == 'qAcc' or $outFile == 'tAcc'
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168 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.led'
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169 #else
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170 #if $outFile == 'qAcc' or $outFile == 'tAcc' or $outFile == 'qPu' or $outFile == 'tPu'
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171 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.lpu'
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172 #else
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173 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.tabular'
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174 #end if
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175 #end if
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176 --out '$curOutFile'
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177 #end for
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178 #end if
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179 #end if
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180 #end if
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181 ]]>
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182 </command>
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183 <inputs>
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184 <conditional name="advancedOptions">
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185 <param label="Options" name="advancedSelector" type="select">
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186 <option value="basic">Basic Options</option>
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187 <option value="advanced">Advanced Options</option>
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188 </param>
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189 <when value="advanced">
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190 <section expanded="True" name="query" title="Query Parameters">
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191 <expand macro="query_macro" />
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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" />
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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" />
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194 </section>
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195 <section expanded="True" name="target" title="Target Parameters">
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196 <expand macro="target_macro" />
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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" />
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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" />
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199 </section>
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200 <section name="seed" title="Seed Parameters">
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201 <expand macro="seed_macro" />
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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" />
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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" />
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204 <param argument="--seedMaxE" help="" label="Max. energy a seed region may have" max="999" min="-999" type="integer" value="0" />
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205 <param argument="--seedMinPu" help="" label="Min. unpaired probability (per sequence)" max="1" min="0" type="float" value="0" />
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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="" />
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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="" />
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208 </section>
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209 <section name="shape" title="SHAPE Input Parameters">
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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" />
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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" />
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212 </section>
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213 <section name="interaction" title="Prediction Parameters">
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214 <expand macro="interaction_macro" />
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215 <param argument="--model" help="Sets what to optimize for" label="Prediction target" type="select">
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216 <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option>
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217 <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option>
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218 <option value="P">Single-site interaction with minimal free ensemble energy per site</option>
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219 </param>
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220 <param argument="--energyVRNA" help="" label="Energy parameter" type="select">
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221 <option value="Turner99">Turner-1999</option>
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222 <option selected="true" value="Turner04">Turner-2004</option>
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223 <option value="Andronescu07">Andronescu-2007</option>
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224 </param>
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225 <param argument="--temperature" help="Temperature scaling of ViennaRNA energy parameters" label="Temperature [Celsius]" max="100" min="0" type="integer" value="37" />
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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" />
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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" />
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228 </section>
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229 <section name="output" title="Output Options">
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230 <expand macro="output_macro" />
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231 <param argument="--outMaxE" help="Only interactions with E ≤ maxE are reported" label="Max. absolute energy of an interaction" type="float" value="0" />
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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" />
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233 <conditional name="add_output_cond">
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234 <param label="Additional output files" name="selector" type="select">
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235 <option value="add">Output additional files</option>
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236 <option selected="true" value="none">Don't output additional files</option>
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237 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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238 <when value="add">
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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">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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240 <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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241 <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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242 <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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243 <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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244 <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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245 <option value="tMinE">For all target indices: minimal energy of any interaction covering the position (tMinE)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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246 <option value="qAcc">The query's ED values (qAcc)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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247 <option value="tAcc">The target's ED values (tAcc) </option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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248 <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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249 <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option>
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250 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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251 </when>
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252 <when value="none" />
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253 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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254 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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255 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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256 <when value="basic">
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257 <section expanded="True" name="query" title="Query Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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258 <expand macro="query_macro" />
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259 </section>
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260 <section expanded="True" name="target" title="Target Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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261 <expand macro="target_macro" />
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262 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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263 <section name="seed" title="Seed Parameters">
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fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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264 <expand macro="seed_macro" />
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33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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265 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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266 <section name="interaction" title="Interaction Parameters">
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267 <expand macro="interaction_macro" />
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268 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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269 <section name="output" title="Output Options">
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270 <expand macro="output_macro" />
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271 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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272 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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273 </conditional>
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274 </inputs>
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275 <outputs>
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276 <data format="tabular" label="IntaRNA on ${on_string}" name="outfile" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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277 <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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278 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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279 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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280 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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281 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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282 'spotProb' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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283 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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284 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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285 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;spotProb.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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286 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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287 <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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288 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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289 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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290 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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291 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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292 'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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293 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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294 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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295 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qSpotProb.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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296 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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297 <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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298 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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299 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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300 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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301 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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302 'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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303 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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304 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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305 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tSpotProb.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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306 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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307 <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list">
0
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308 <filter>
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309 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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310 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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311 advancedOptions['output']['add_output_cond']['selector'] == "add" and
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312 'qMinE' in advancedOptions['output']['add_output_cond']['add_output']
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313 ))
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314 </filter>
7
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diff changeset
315 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qMinE.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
316 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
317 <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
318 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
319 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
320 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
321 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
322 'tMinE' in advancedOptions['output']['add_output_cond']['add_output']
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
323 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
324 </filter>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
325 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tMinE.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
326 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
327 <collection label="For all index combinations: minimal energy of any interaction covering the index pair, on ${on_string}" name="pMinE_output" type="list">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
328 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
329 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
330 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
331 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
332 'pMinE' in advancedOptions['output']['add_output_cond']['add_output']
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
333 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
334 </filter>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
335 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;pMinE.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
336 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
337 <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
338 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
339 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
340 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
341 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
342 'qAcc' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
343 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
344 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
345 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qAcc.*)\.led" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
346 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
347 <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
348 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
349 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
350 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
351 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
352 'tAcc' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
353 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
354 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
355 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\.led" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
356 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
357 <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
358 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
359 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
360 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
361 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
362 'qPu' in advancedOptions['output']['add_output_cond']['add_output']
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
363 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
364 </filter>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
365 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\.lpu" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
366 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
367 <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
368 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
369 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
370 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
371 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
372 'tPu' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
373 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
374 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
375 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\.lpu" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
376 </collection>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
377 </outputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
378 <tests>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
379 <test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
380 <conditional name="advancedOptions">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
381 <param name="advancedSelector" value="basic" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
382 <section name="query">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
383 <param name="query" value="intarna_query.fa" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
384 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
385 <section name="target">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
386 <param name="target" value="intarna_target.fa" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
387 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
388 </conditional>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
389 <output file="intarna_result.tabular" name="outfile" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
390 </test>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
391 <test>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
392 <conditional name="advancedOptions">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
393 <param name="advancedSelector" value="advanced" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
394 <section name="query">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
395 <param name="query" value="intarna_query.fa" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
396 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
397 <section name="target">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
398 <param name="target" value="intarna_target.fa" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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399 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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400 <section name="output">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
401 <conditional name="add_output_cond">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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diff changeset
402 <param name="selector" value="add" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
403 <param name="add_output" value="spotProb,qMinE,tAcc,qPu" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
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404 </conditional>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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405 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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406 </conditional>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
407 <output file="intarna_result.tabular" name="outfile" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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diff changeset
408 <output_collection count="4" name="spotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
409 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
410 <output_collection count="4" name="qMinE_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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diff changeset
411 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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412 <output_collection count="2" name="qPu_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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diff changeset
413 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
414 <output_collection count="2" name="tAcc_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
415 </output_collection>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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diff changeset
416 </test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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417 </tests>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
418 <help><![CDATA[
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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419
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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420 **What it does**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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421 Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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422 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.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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423 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.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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diff changeset
424 .. class:: infomark
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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diff changeset
425 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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426 **Input**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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427 RNA sequences in *FASTA* format
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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428 **Output**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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429 RNA-RNA interaction information in CSV format and additional information/files on demand
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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430
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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431 ]]>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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432 </help>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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433 <citations>
3
03c09b961567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 0d69e178bbd7019a51a50fda5e5cf6721770083d
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434 <citation type="doi">10.1093/nar/gkx279</citation>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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435 <citation type="doi">10.1093/nar/gku359</citation>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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436 <citation type="doi">10.1093/bioinformatics/btn544</citation>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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437 </citations>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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438 </tool>