annotate intarna.xml @ 1:34de9855c962 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 8f81e944ec7edd1777f0eb679b8a425e4f58b69e-dirty
author rnateam
date Thu, 07 Sep 2017 08:47:05 -0400
parents 33c0836ea386
children 4616bc52f157
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34de9855c962 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 8f81e944ec7edd1777f0eb679b8a425e4f58b69e-dirty
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1 <tool id="intarna" name="IntaRNA" version="2.0.4">
0
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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 name="_query" argument="--query" format="fasta" type="data" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" />
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6 <conditional name="qAcc_cond">
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7 <param argument="--qAcc" type="select" label="Accessibility computation" help="">
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8 <option value="N">No accessibility contributions ('N')</option>
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9 <option value="C" selected="true">Computation of accessibilities ('C')</option>
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10 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
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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="text" type="data" label="Accessibility computation" help="" />
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17 </when>
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18 <when value="E">
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19 <param argument="--qAccFile" format="text" type="data" label="Accessibility computation" help="" />
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20 </when>
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21 </conditional>
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22 <param argument="--qAccW" type="integer" value="150" min="0" max="99999"
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23 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
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24 <param argument="--qAccL" type="integer" value="100" min="0" max="99999"
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25 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW'"/>
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26 </macro>
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27 <macro name="target_macro">
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28 <param name="_target" argument="--target" format="fasta" type="data" label="Target sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" />
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29 <conditional name="tAcc_cond">
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30 <param argument="--tAcc" type="select" label="Accessibility computation" help="">
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31 <option value="N">No accessibility contributions ('N')</option>
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32 <option value="C" selected="true">Computation of accessibilities ('C')</option>
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33 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
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34 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
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35 </param>
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36 <when value="N"/>
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37 <when value="C"/>
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38 <when value="P">
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39 <param argument="--tAccFile" format="text" type="data" label="The file to be parsed" help="... for accessibility computation" />
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40 </when>
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41 <when value="E">
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42 <param argument="--tAccFile" format="text" type="data" label="Accessibility computation" help="" />
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43 </when>
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44 </conditional>
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45 <param argument="--tAccW" type="integer" value="150" min="0" max="99999"
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46 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
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47 <param argument="--tAccL" type="integer" value="100" min="0" max="99999"
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48 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'tAccW'"/>
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49 </macro>
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50 <macro name="seed_macro">
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51 <param argument="--noSeed" truevalue="--noSeed" falsevalue="" checked="False" type="boolean"
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52 label="Disable seed constraint entirely for computation" help=""/>
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53 <param argument="--seedBP" type="integer" value="7" min="2" max="20" label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/>
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54 <param argument="--seedMaxUP" type="integer" value="0" min="0" max="20"
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55 label="Max. overall number of unpaired bases (query+target)" help=""/>
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56 </macro>
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57 <macro name="interaction_macro">
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58 <param argument="--mode" type="select" label="Prediction mode" help="">
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59 <option value="H" selected="true">Heuristic (fast and low memory)</option>
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60 <option value="M">Exact and low memory</option>
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61 <option value="E">Exact (high memory)</option>
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62 </param>
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63 </macro>
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64 <macro name="output_macro">
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65 <param argument="--outMode" type="select" label="Output Mode" help="">
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66 <option value="N">Normal output (ASCII char + energy)</option>
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67 <option value="D">Detailed output (ASCII char + energy/position details)</option>
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68 <option value="C" selected="true">CSV output (see --outCsvCols)</option>
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69 <option value="1">backward compatible IntaRNA v1.* normal output</option>
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70 <option value="O">backward compatible IntaRNA v1.* detailed output</option>
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71 </param>
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72
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73
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74 <param argument="--outCsvCols" type="text" optional="true"
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75 label="Comma separated list of CSV column IDs to print" help="An empty argument prints all possible columns from the following available ID list: [id1], [id2], [seq1], [seq2], [subseq1], [subseq2], [subseqDP], [subseqDB], [start1], [end1], [start2], [end2], [hybridDP], [hybridDB], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2]"/>
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76 <param argument="--outNumber" type="integer" value="1" min="0" max="1000"
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77 label="Max. number of predictions per query/target pair" help="Number of optimal and suboptimal interaction to predict per query-target pair"/>
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78 <param argument="--outOverlap" type="select" label="Overlapping of suboptimal predictions" help="Whether or not interactions can overlap">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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79 <option value="N" >in none of the sequences</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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80 <option value="T">in the target only</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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81 <option value="Q" selected="true">in the query only</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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82 <option value="B">in both sequences</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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83 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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84 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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85 </macros>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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86 <requirements>
1
34de9855c962 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 8f81e944ec7edd1777f0eb679b8a425e4f58b69e-dirty
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87 <requirement type="package" version="2.0.4">intarna</requirement>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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88 </requirements>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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89 <stdio>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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90 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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91 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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92 </stdio>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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93 <version_command>IntaRNA --version</version_command>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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94 <command>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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95 <![CDATA[
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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96 IntaRNA
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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97 #if $advancedOptions.advancedSelector == "advanced"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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98 ## Query parameters
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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99 --query '$advancedOptions.query._query'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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100 --qAcc $advancedOptions.query.qAcc_cond.qAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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101 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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102 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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103 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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104 --qAccW $advancedOptions.query.qAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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105 --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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106 ## #if $advancedOptions.query.qAccConstr <> "."
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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107 ## --qAccConstr $advancedOptions.query.qAccConstr
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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108 ## #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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109 --qIntLoopMax $advancedOptions.query.qIntLoopMax
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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110 #if $advancedOptions.query.qRegion
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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111 --qRegion '$advancedOptions.query.qRegion'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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112 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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113
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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114 ## Target param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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115 --target '$advancedOptions.target._target'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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116 --tAcc $advancedOptions.target.tAcc_cond.tAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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117 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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118 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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119 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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120 --tAccW $advancedOptions.target.tAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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121 --tAccL $advancedOptions.target.tAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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122 ## #if $advancedOptions.target.tAccConstr <> "."
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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123 ## --tAccConstr $advancedOptions.target.tAccConstr
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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124 ## #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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125 --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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126 #if $advancedOptions.target.tRegion
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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127 --tRegion '$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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128 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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129
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130 ## Seed param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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131 --noSeed $advancedOptions.seed.noSeed
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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132 --seedBP $advancedOptions.seed.seedBP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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133 --seedMaxUP $advancedOptions.seed.seedMaxUP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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134 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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135 --seedTMaxUP $advancedOptions.seed.seedTMaxUP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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136 --seedMaxE $advancedOptions.seed.seedMaxE
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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137 --seedMinPu $advancedOptions.seed.seedMinPu
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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138 --seedQRange '$advancedOptions.seed.seedQRange'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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139 --seedTRange '$advancedOptions.seed.seedTRange'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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140
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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141 ## Interaction param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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142 --mode $advancedOptions.interaction.mode
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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143 --pred $advancedOptions.interaction.pred
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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144 --energy $advancedOptions.interaction.energy
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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145 #if $advancedOptions.interaction.energyVRNA
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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146 --energyVRNA '$advancedOptions.interaction.energyVRNA'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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147 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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148 --temperature $advancedOptions.interaction.temperature
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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149
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150 ##Output param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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151 --out ./temp_tabular_output
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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152 --outMode $advancedOptions.output.outMode
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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153 --outNumber $advancedOptions.output.outNumber
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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154 --outOverlap $advancedOptions.output.outOverlap
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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155 --outMaxE $advancedOptions.output.outMaxE
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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156 --outDeltaE $advancedOptions.output.outDeltaE
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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157 #if $advancedOptions.output.outCsvCols
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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158 --outCsvCols '$advancedOptions.output.outCsvCols'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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159 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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160 #if $advancedOptions.output.add_output_cond.selector == "add"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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161 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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162 #for j in $advancedOptions.output.add_output_cond.add_output.value:
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163 --$j $getVar($j)
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164 #end for
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165 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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166 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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167
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168 #elif $advancedOptions.advancedSelector == "basic"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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169 ## Query parameters
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170 --query '$advancedOptions.query._query'
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171 --qAcc $advancedOptions.query.qAcc_cond.qAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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172 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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173 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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174 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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175 --qAccW $advancedOptions.query.qAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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176 --qAccL $advancedOptions.query.qAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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177
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178 ## Target param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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179 --target '$advancedOptions.target._target'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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180 --tAcc $advancedOptions.target.tAcc_cond.tAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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181 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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182 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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183 #end if
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184 --tAccW $advancedOptions.target.tAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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185 --tAccL $advancedOptions.target.tAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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186
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187 ## Seed param.
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188 --noSeed $advancedOptions.seed.noSeed
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189 --seedBP $advancedOptions.seed.seedBP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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190 --seedMaxUP $advancedOptions.seed.seedMaxUP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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191
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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192 ## Interaction param.
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193 --mode $advancedOptions.interaction.mode
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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194
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195 ##Output param.
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196 --out ./temp_tabular_output
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197 --outMode $advancedOptions.output.outMode
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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198 --outNumber $advancedOptions.output.outNumber
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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199 --outOverlap $advancedOptions.output.outOverlap
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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200 #if $advancedOptions.output.outCsvCols
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201 --outCsvCols '$advancedOptions.output.outCsvCols'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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202 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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203 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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204 && sed 's/\t/ /g' ./temp_tabular_output > ./temp_output_no_tabs
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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205 && sed 's/;/\t/g' ./temp_output_no_tabs > '$outfile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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206
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207 ]]>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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208 </command>
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209 <inputs>
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210
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211 <conditional name="advancedOptions">
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212 <param name="advancedSelector" type="select" label="Options">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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213 <option value="basic">Basic Options</option>
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214 <option value="advanced">Advanced Options</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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215 </param>
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216 <when value="advanced">
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217 <section name="query" title="Query Parameters" expanded="True">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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218 <expand macro="query_macro"/>
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219 <!--
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220 <param name="qAccConstr" type="select" label="Structure constraint for each sequence position" help="">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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221 <option value="." selected="true">No constraint</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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222 <option value="x">Unpaired</option>
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223 <option value="b">Blocked positions are excluded from interaction prediction and considered unpaired </option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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224 </param>
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225 -->
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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226 <param argument="--qIntLoopMax" type="integer" value="16" min="0" max="30"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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227 label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the query"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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228 <param argument="--qRegion" type="text" optional="true" label="Query regions to be considered for interaction prediction"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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229 help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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230 </section>
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231 <section name="target" title="Target Parameters" expanded="True">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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232 <expand macro="target_macro"/>
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233 <!-- <param name="tAccConstr" type="select" label="Structure constraint for each sequence position" help="">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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234 <option value="." selected="true">No constraint</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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235 <option value="x">Unpaired</option>
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236 <option value="b">Blocked.blocked positions are excluded from interaction prediction and considered unpaired </option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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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 -->
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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239
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240 <param argument="--tIntLoopMax" type="integer" value="16" min="0" max="30"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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241 label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the target"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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242 <param argument="--tRegion" type="text" optional="true" label="Target regions to be considered for interaction prediction"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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243 help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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244 </section>
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245 <section name="seed" title="Seed Parameters">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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246 <expand macro="seed_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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247 <param argument="--seedQMaxUP" type="integer" value="-1" min="-1" max="20"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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248 label="Max. number of unpaired bases within the query's seed region" help=""/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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249 <param argument="--seedTMaxUP" type="integer" value="-1" min="-1" max="20"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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250 label="Max. number of unpaired bases within the target's seed region" help=""/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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251 <param argument="--seedMaxE" type="integer" value="0" min="-999" max="999"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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252 label="Max. energy a seed region may have" help=""/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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253 <param argument="--seedMinPu" type="float" value="0" min="0" max="1"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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254 label="Min. unpaired probability (per sequence)" help=""/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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255
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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256 <param argument="--seedQRange" type="text" value=""
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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257 label="Interval(s) in the query to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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258 <param argument="--seedTRange" type="text" value=""
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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259 label="Interval(s) in the target to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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260 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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261 <section name="interaction" title="Interaction Parameters">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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262 <expand macro="interaction_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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263 <param argument="--pred" type="select" label="Prediction target" help="Sets what to optimize for">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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264 <option value="S" selected="true">Single-site minimum-free-energy interaction</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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265 <option value="P">Single-site maximum-probability interaction</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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266 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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267 <param argument="--energy" type="select" label="Energy computation" help="">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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268 <!-- <option value="B">Base pair == -1 ()</option> -->
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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269 <option value="V" selected="true">VRNA-based computation</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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270 </param>
1
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271 <param argument="--energyVRNA" type="data" format="txt" optional="true"
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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272 label="Energy parameter file of VRNA package" help="If not provided, the default parameter set of the linked Vienna RNA package is used."/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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273 <param argument="--temperature" type="integer" value="37" min="0" max="100"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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274 label="Temperature [°C]" help="VRNA energy parameters"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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275 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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276 <section name="output" title="Output Options">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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277 <expand macro="output_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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278 <param argument="--outMaxE" type="float" value="0"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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279 label="Max. absolute energy of an interaction" help="Only interactions with E &#8804; maxE are reported"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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280 <param argument="--outDeltaE" type="float" value="100"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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281 label="Max. delta energy above mfe of an interaction" help="suboptimal output: only interactions with E &#8804; (minE+deltaE) are reported"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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282
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283 <conditional name="add_output_cond">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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284 <param name="selector" type="select" label="Additional output files">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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285 <option value="add">Output additional files</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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286 <option value="none" selected="true">Don't output additional files</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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287 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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288 <when value="add">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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289 <param name="add_output" type="select" display="checkboxes" multiple="True"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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290 label="Additional output files" help="Written in a format similar to RNAplfold unpaired probability output.">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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291 <option value="outQAccFile" selected="true">The query's ED values (--outQAccFile)</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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292 <option value="outTAccFile">The target's ED values (--outTAccFile) </option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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293 <option value="outQPuFile">The query's unpaired probabilities used for ED values (--outQPuFile) </option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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294 <option value="outTPuFile">The target's unpaired probabilities used for ED values (--outTPuFile)</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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295 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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296 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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297 <when value="none"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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298 </conditional>
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299
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300 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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301 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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302 <when value="basic">
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303 <section name="query" title="Query Parameters" expanded="True">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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304 <expand macro="query_macro"/>
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305 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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306 <section name="target" title="Target Parameters" expanded="True">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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307 <expand macro="target_macro"/>
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308 </section>
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309 <section name="seed" title="Seed Parameters">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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310 <expand macro="seed_macro"/>
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311 </section>
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312 <section name="interaction" title="Interaction Parameters">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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313 <expand macro="interaction_macro"/>
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314 </section>
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315 <section name="output" title="Output Options">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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316 <expand macro="output_macro"/>
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317 </section>
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318 </when>
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319 </conditional>
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320 </inputs>
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321 <outputs>
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322 <data name="outfile" format="text" label="IntaRNA on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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323 <change_format>
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324 <when input="advancedOptions.output.outMode" value="C" format="tabular" />
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325 </change_format>
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326 </data>
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327 <data name="outQAccFile" format="text" label="Query's ED values, on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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328 <filter>
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329 ((
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330 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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diff changeset
331 advancedOptions['output']['add_output_cond']['selector'] == "add" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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332 'outQAccFile' in advancedOptions['output']['add_output_cond']['add_output']
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333 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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334 </filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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335 </data>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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336 <data name="outTAccFile" format="text" label="Target's ED values, on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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337 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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338 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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339 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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340 advancedOptions['output']['add_output_cond']['selector'] == "add" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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341 'outTAccFile' in advancedOptions['output']['add_output_cond']['add_output']
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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342 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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343 </filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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344 </data>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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345 <data name="outQPuFile" format="text" label="Query's unpaired probabilities used for ED values, on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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346 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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347 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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348 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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349 advancedOptions['output']['add_output_cond']['selector'] == "add" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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350 'outQPuFile' in advancedOptions['output']['add_output_cond']['add_output']
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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351 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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352 </filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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353 </data>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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354 <data name="outTPuFile" format="text" label="Target's unpaired probabilities used for ED values, on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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355 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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356 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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357 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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358 advancedOptions['output']['add_output_cond']['selector'] == "add" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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359 'outTPuFile' in advancedOptions['output']['add_output_cond']['add_output']
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360 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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361 </filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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362 </data>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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363 </outputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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364 <tests>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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365 <test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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366 <conditional name="advancedOptions">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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367 <param name="advancedSelector" value="basic"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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368 <section name="query">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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369 <param name="_query" value="intarna_query.fa" />
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370 </section>
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371 <section name="target">
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372 <param name="_target" value="intarna_target.fa"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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373 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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374 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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375 <output name="outfile" file="intarna_result.tabular"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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376 </test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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377 </tests>
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378
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379 <help>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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380 <![CDATA[
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381
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382 **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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383
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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384 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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385
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386 During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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387
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388 IntaRNA, developed by `Prof. Backofen's bioinformatics group at Freiburg University <http://www.bioinf.uni-freiburg.de/>`_, is a general and fast approach to the prediction of RNA-RNA interactions incorporating both the accessibility of interacting sites as well as the existence of a user-definable seed interaction. We successfully applied IntaRNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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389
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390 .. class:: infomark
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391
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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392 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information.
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393
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394
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395 **Input**
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396
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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397
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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398
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399 RNA sequences in *FASTA* format
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400
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401
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402 **Output**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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403
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404 RNA-RNA interaction information in CSV format and additional information/files on demand
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405
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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406 ]]>
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407
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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408 </help>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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409
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410 <citations>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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411 <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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412 <citation type="doi">10.1093/bioinformatics/btn544</citation>
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413 </citations>
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414
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415 </tool>