Mercurial > repos > rnateam > locarna_exparnap

annotate locarna_exparnap.xml @ 0:e91e4f48875e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
author rnateam
date Fri, 13 Jan 2017 16:49:16 -0500
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children e66514da3a99
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0
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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1 <tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@VERSION@.0">
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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2 <description>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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3 Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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4 </description>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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5
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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6 <macros>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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7 <import>macros.xml</import>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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8 </macros>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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9
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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10 <expand macro="requirements" />
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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11
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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12 <expand macro="stdio" />
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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13
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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14 <expand macro="version" />
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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16 <command><![CDATA[
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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17 exparna_p
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18
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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19 '$inputA'
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20 '$inputB'
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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21
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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22 ## -------------------- scoring parameters
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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23 #
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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24 $Scoring.no_stacking
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25 --alpha_1 $Scoring.alpha_1
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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26 --alpha_2 $Scoring.alpha_2
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27 --alpha_3 $Scoring.alpha_3
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28 --struct-mismatch-score $Scoring.struct_mismatch_score
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29
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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30 @HEURISTIC_ARGS@
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31 --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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32 --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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33
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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34 @CONSTRAINT_ARGS@
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35
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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36 ## -------------------- other parameters
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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37 #
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38 #if str($Other.subopt.subopt_selector) == "on"
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39 --diff-to-opt-score $Other.subopt.diff_to_opt_score
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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40 --number-of-EPMs $Other.subopt.number_of_EPMs
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41 #end if
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42
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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43 --min-score $Other.min_score
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44
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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45 $Other.inexact_struct_match
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46 $Other.add_filter
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47 $Other.no_chaining
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48 --out-min-prob $Other.out_min_prob
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49
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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50 ## -------------------- output
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51
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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52 #if 'postscript' in str($outputs).split(",")
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53 --output-ps
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54 --PS_fileA '$ps_fileA'
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55 --PS_fileB '$ps_fileB'
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56 #end if
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57
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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58 #if 'anchors-fasta' in str($outputs).split(",")
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59 --output-locarna '$anchors_fasta'
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60 #end if
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61
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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62 #if 'anchors-pp' in str($outputs).split(",")
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63 --output-anchor-pp anchors_pp
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64 #end if
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65
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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66 #if 'clustal' in str($outputs).split(",")
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67 --output-clustal '$clustal'
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68 #end if
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69
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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70 #if 'epm_list' in str($outputs).split(",")
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71 --output-epm-list '$epm_list'
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72 #end if
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73
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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74 #if 'chained_epm_list' in str($outputs).split(",")
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75 --output-chained-epm-list '$chained_epm_list'
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76 #end if
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77
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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78 @STDOUT_ARGS@
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79
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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80 ## -------------------- post processing
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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81
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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82 #if 'anchors-pp' in str($outputs).split(",")
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83 && mv anchors_pp_A.pp '$anchors_ppA'
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84 && mv anchors_pp_B.pp '$anchors_ppB'
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85 #end if
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86
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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87 ]]></command>
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88
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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89 <inputs>
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90 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
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91 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
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92 />
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93 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
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94 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
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95 />
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96
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97 <param name="outputs" type="select" display="checkboxes" multiple="True"
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98 label="Output options">
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99 <option value="postscript" selected="False">Best EPM chain
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100 as colored postscript</option>
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101 <option value="anchors-fasta" selected="False">Fasta with anchor
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102 constraints from chaining</option>
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103 <option value="anchors-pp" selected="False">LocARNA PP
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104 files merging input PPs and anchor constraints from
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105 chaining</option>
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106 <option value="clustal" selected="False">Chain as
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107 alignment in Clustal format</option>
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108 <option value="epm_list" selected="False">List of the found EPMs</option>
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109 <option value="chained_epm_list" selected="False">List of
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110 EPMs in the best chain</option>
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111 </param>
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112
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113 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
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114 <option value="--quiet">Don't report standard
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115 output</option>
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116 <option value="" selected="True">Non verbose</option>
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117 <option value="--verbose">Verbose</option>
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118 </param>
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119
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120 <section name="Scoring" title="Scoring parameters">
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121 <param argument="alpha_1"
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122 type="integer" value="1" min="0" max="50"
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123 label="Sequence score factor"
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124 />
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125 <param argument="alpha_2"
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126 type="integer" value="5" min="0" max="50"
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127 label="Structure score factor"
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128 />
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129 <param name="no_stacking" argument="no-stacking" type="boolean"
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130 truevalue="" falsevalue="--no-stacking"
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131 label="Add stacking terms"
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132 />
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133 <param argument="alpha_3"
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134 type="integer" value="5" min="0" max="50"
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135 label="Stacking score factor"
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136 />
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137 <param name="struct_mismatch_score" argument="struct-mismatch-score"
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138 type="integer" value="-10" min="-100" max="0"
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139 label="Score for nucleotide mismatch in base pair match"
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140 />
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141 </section>
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142
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143 <section name="Folding" title="RNA folding parameters">
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144 <expand macro="common_folding_parameters" />
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145 </section>
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146
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147 <section name="Heuristics" title="Heuristic parameters">
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148 <expand macro="common_heuristic_parameters" />
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149 <expand macro="max_diff_parameters" />
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150 <expand macro="in_loop_ratio_parameters" />
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151 <expand macro="exparnap_in_loop_parameters" />
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152 </section>
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153
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154 <section name="Constraints" title="Constraint parameters">
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155 <expand macro="common_constraint_parameters" />
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156 </section>
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157
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158
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159 <section name="Other" title="Other parameters">
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160 <conditional name="subopt">
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161 <param name="subopt_selector" type="select"
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162 label="Suboptimal traceback of EPMs (exact pattern matches)"
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163 help="(--subopt)">
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164 <option value="off">Enumerate only optimal
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165 EPMs</option>
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166 <option value="on">Perform suboptimal traceback of EPMs</option>
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167 </param>
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168 <when value="off" />
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169 <when value="on">
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170 <param name="diff_to_opt_score" argument="diff-to-opt-score"
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171 type="integer" value="-1" min="-20" max="0"
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172 label="Maximum score difference to optimum" />
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173 <param name="number_of_EPMs" argument="number-of-EPMs"
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174 type="integer" value="100" min="1" max="10000"
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175 label="Maximal number of EPMs" />
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176 </when>
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177 </conditional>
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178
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179 <param name="min_score" argument="min-score"
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180 type="integer" value="30" min="0" max="1000"
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181 label="Minimum score of EPM" />
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182
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183 <param name="inexact_struct_match" argument="inexact-struct-match" type="boolean"
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184 truevalue="--inexact-struct-match" falsevalue=""
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185 label="Allow inexact structure matches"/>
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186
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187 <param name="add_filter" argument="add-filter" type="boolean"
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188 truevalue="--add-filter" falsevalue="" checked="False"
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189 label="Apply an additional filter to enumerate only
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190 EPMs that are maximally extended (only inexact)"/>
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191
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192 <param name="no_chaining" argument="no-chaining" type="boolean"
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193 truevalue="" falsevalue="--no-chaining" checked="True"
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194 label="Find best overall chain by chaining"/>
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195
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196 <param name="out_min_prob" argument="out-min-prob"
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197 type="float" value="0.0005" min="0" max="1"
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198 label="Minimal probability in output (min-prob overrides if smaller)"/>
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199
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200 </section>
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201 </inputs>
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202
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203 <outputs>
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204 <expand macro="standard_outupt" />
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205 <data format="ps" name="ps_fileA"
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206 label="${tool.name} chain in RNA 1 (postscript) on ${on_string}">
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207 <filter>'postscript' in outputs</filter>
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208 </data>
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209 <data format="ps" name="ps_fileB"
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210 label="${tool.name} chain in RNA 2 (postscript) on ${on_string}">
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211 <filter>'postscript' in outputs</filter>
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212 </data>
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213 <data format="txt" name="anchors_fasta"
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214 label="${tool.name} anchor constraints from chain (fasta) on ${on_string}">
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215 <filter>'anchors-fasta' in outputs</filter>
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216 </data>
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217 <data format="txt" name="anchors_ppA"
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218 label="${tool.name} anchors for RNA 1 (pp) on ${on_string}">
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219 <filter>'anchors-pp' in outputs</filter>
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220 </data>
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221 <data format="txt" name="anchors_ppB"
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222 label="${tool.name} anchors for RNA 2 (pp) on ${on_string}">
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223 <filter>'anchors-pp' in outputs</filter>
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224 </data>
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225 <data format="clustal" name="clustal"
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226 label="${tool.name} chain as alignment (clustal) on ${on_string}">
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227 <filter>'clustal' in outputs</filter>
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228 </data>
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229 <data format="tabular" name="epm_list"
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230 label="${tool.name} list of epms on ${on_string}">
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231 <filter>'epm_list' in outputs</filter>
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232 </data>
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233 <data format="tabular" name="chained_epm_list"
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234 label="${tool.name} list of epms in chain on ${on_string}">
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235 <filter>'chained_epm_list' in outputs</filter>
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236 </data>
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237 </outputs>
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238
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239 <tests>
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240 <test>
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241 <param name="inputA" value="tRNA_2-1.fa" />
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242 <param name="inputB" value="tRNA_2-2.fa" />
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243 <param name="outputs" value="epm_list" />
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244 <output name="epm_list" file="tRNA_2.epms" />
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245 </test>
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246 </tests>
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247
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248 <help><![CDATA[ **LocARNA -- Pairwise matching and folding of RNAs (ExpARNA-P)**
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249
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250 Pairwise matching and folding tool of the LocARNA suite (ExpARNA-P).
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251
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252 **Input.**
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253
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254 Input consists of two sequences or alignments, which are specified in
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255 fasta, clustal, stockholm, or LocARNA pp format.
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256
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257 Optionally, one can specify structure and anchor constraints in these
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258 input files.b
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259
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260 **Output.**
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261
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262 The program enumerates exactly matching local substructures (exact
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263 pattern matches = EPMs) and optionally chains them. It returns lists
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264 of chained and unchained matches, visualizations of the results and
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265 anchor constraints for alignment.
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266
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267
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268 For more information, see
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269 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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270 ]]></help>
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272 <expand macro="citations" />
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274 </tool>