Mercurial > repos > rnateam > locarna_pairwise

annotate locarna_pairwise.xml @ 3:f3f08a777c10 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 14:29:12 +0000
parents 433601e9f132
children 4839df2b2f6b
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f3f08a777c10 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
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1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>
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3 Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse)
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4 </description>
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5
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6 <macros>
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7 <import>macros.xml</import>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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8 </macros>
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9
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10 <expand macro="requirements" />
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11
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12 <expand macro="stdio" />
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13
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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14 <expand macro="version" />
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16 <command><![CDATA[
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17 #if str($alignment_mode.alignment_mode_selector) == "sparse"
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18 sparse
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19 #else
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20 locarna
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21 #end if
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23 '$inputA'
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24 '$inputB'
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25
3
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26 ## --width 60
0
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27
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28 ## -------------------- alignment mode and specific options
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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29
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30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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31 #if str($alignment_mode.free_endgaps) != "----"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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32 --free-endgaps $alignment_mode.free_endgaps
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33 #end if
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34 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
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35 --sequ-local on
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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36 #else if str($alignment_mode.alignment_mode_selector) == "structure_local_locarna"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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37 --struct-local on
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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38 #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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39 --sequ-local on
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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40 --struct-local on
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41 #end if
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42
1
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43 @SCORING_ARGS@
0
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44
1
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45 @FOLDING_ARGS@
0
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46 $Folding.alifold_consensus_dp
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47 --consensus-structure $Folding.consensus_structure
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48
1
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49 @HEURISTIC_ARGS@
0
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50
2
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51 #if str($alignment_mode.alignment_mode_selector) == "sparse"
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52 @HEURISTIC_SPARSE_ARGS@
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53 #end if
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54
1
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55 @CONSTRAINT_ARGS@
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56
0
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57 ## -------------------- output
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58
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59 #if 'stockholm' in str($outputs).split(",")
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60 --stockholm '$stockholm'
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61 #end if
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62 #if 'clustal' in str($outputs).split(",")
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63 --clustal '$clustal'
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64 #end if
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65 #if 'clustal_strict' in str($outputs).split(",") and (not 'clustal' in str($outputs).split(","))
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66 --clustal '$clustal_strict'
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67 #end if
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68 #if 'pp' in str($outputs).split(",")
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69 --pp '$pp'
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70 #end if
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71
1
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72 @STDOUT_ARGS@
0
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74 #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",")
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75 && cp $clustal $clustal_strict
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76 #end if
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77
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78 #if 'clustal_strict' in str($outputs).split(",")
1
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79 && cp '$clustal_strict' '$clustal_strict~'
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80 && sed '/^#/d' '$clustal_strict~' >'$clustal_strict'
0
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81 #end if
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82
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83 ]]></command>
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84
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85 <inputs>
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86 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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87 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
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88 />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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89 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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90 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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91 />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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92 <conditional name="alignment_mode">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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93 <param name="alignment_mode_selector" type="select" label="Alignment mode"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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94 help="Note that local alignment mode usually requires to turn off
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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95 the 'max-diff' heuristic (maximal difference for alignment traces)."
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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96 >
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97 <option value="global_locarna">Global alignment
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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98 (LocARNA)</option>
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99 <option value="local_locarna">Local alignment (LocARNA)</option>
2
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100 <option value="sparse">Global fast alignment (SPARSE)</option>
0
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101 <option value="structure_sequence_local_locarna">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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102 Structure and sequence local alignment (LocARNA)
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103 </option>
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104 <option value="structure_local_locarna">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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105 Structure local, sequence global alignment (LocARNA)
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106 </option>
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107 </param>
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108 <when value="global_locarna">
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109 <param name="free_endgaps" type="select" label="Free endgaps"
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110 help="Specify whether gaps at the ends (all, 5', or 3' ends)
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111 of the sequences should be penalized or allowed for free.">
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112 <option value="----">None</option>
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113 <option value="++++">All</option>
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114 <option value="+-+-">5' ends</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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115 <option value="-+-+">3' ends</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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116 <option value="++--">first sequence</option>
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117 <option value="--++">second sequence</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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118 <option value="+---">sequence A, 5' end</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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119 <option value="-+--">sequence A, 3' end</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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120 <option value="--+-">sequence B, 5' end</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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121 <option value="---+">sequence B, 3' end</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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122 </param>
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123 </when>
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124 <when value="local_locarna">
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125 </when>
2
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126 <when value="sparse">
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127 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">
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128 <expand macro="common_heuristic_parameters_sparse" />
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129 </section>
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130
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131 </when>
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132
0
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133 <when value="structure_sequence_local_locarna" />
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134 <when value="structure_local_locarna" />
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135 </conditional>
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136
3
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137 <param name="outputs" type="select" display="checkboxes" multiple="true"
0
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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138 label="Output options">
3
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139 <option value="clustal_strict" selected="true">Output alignment
0
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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140 in ClustalW format</option>
3
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141 <option value="clustal" selected="false">Output alignment
0
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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142 in constraint-annotated ClustalW format</option>
3
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143 <option value="stockholm" selected="false">Output
0
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144 alignment in Stockholm format</option>
3
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145 <option value="pp" selected="false">Output
0
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146 alignment in LocARNA's PP 2.0 format</option>
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147 </param>
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148
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149 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
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150 <option value="--quiet">Don't report standard
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151 output</option>
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152 <option value="">Non verbose</option>
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153 <option value="--verbose">Verbose</option>
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154 </param>
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155
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156 <section name="Scoring" title="Scoring parameters">
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157 <expand macro="common_scoring_parameters" />
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158 </section>
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159
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160 <section name="Folding" title="RNA folding parameters">
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161 <expand macro="common_folding_parameters" />
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162 <expand macro="alifold_consensus_parameter" />
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163 <param name="consensus_structure" type="select" label="Consensus structure type"
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164 help="Type of consensus structures written to screen and stockholm output"
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165 >
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166 <!-- <option value="mea">mea</option>-->
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167 <option value="none">none</option>
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168 <option value="alifold">alifold</option>
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169 </param>
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170 </section>
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171
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172 <section name="Heuristics" title="Heuristic parameters">
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173 <expand macro="common_heuristic_parameters" />
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174 <expand macro="max_diff_parameters_aln" />
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175 </section>
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176
1
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177 <section name="Constraints" title="Constraint parameters">
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178 <expand macro="common_constraint_parameters" />
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179 </section>
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180 </inputs>
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181
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182 <outputs>
1
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183 <expand macro="standard_outupt" />
0
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184 <data format="clustal" name="clustal"
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185 label="${tool.name} on ${on_string}: alignment (annotated clustal)">
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186 <filter>'clustal' in outputs</filter>
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187 </data>
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188 <data format="clustal" name="clustal_strict"
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189 label="${tool.name}on ${on_string}: alignment (clustal)">
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190 <filter>'clustal_strict' in outputs</filter>
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191 </data>
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192 <data format="stockholm" name="stockholm"
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193 label="${tool.name} on ${on_string}: alignment (stockholm)">
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194 <filter>'stockholm' in outputs</filter>
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195 </data>
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196 <data format="txt" name="pp"
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197 label="${tool.name} on ${on_string}: alignment (PP 2.0)">
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198 <filter>'pp' in outputs</filter>
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199 </data>
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200 </outputs>
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201
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202 <tests>
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203 <test expect_num_outputs="1">
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204 <param name="inputA" value="tRNA_2-1.fa" />
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205 <param name="inputB" value="tRNA_2-2.fa" />
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206 <param name="outputs" value="clustal" />
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207 <output name="clustal" file="tRNA_2.aln" lines_diff="2" />
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208 </test>
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209 <test expect_num_outputs="2">
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210 <param name="inputA" value="haca.snoRNA-1.aln" />
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211 <param name="inputB" value="haca.snoRNA-2.aln" />
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212 <param name="outputs" value="clustal_strict,clustal" />
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213 <output name="clustal" file="haca.snoRNA-c.aln" lines_diff="2" />
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214 <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="2" />
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215 </test>
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216 </tests>
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217
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218 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs**
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219
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220 Pairwise RNA alignment tools of the LocARNA suite (locarna,
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221 sparse). These tools perform variants of simultaneous RNA folding and
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222 alignment. They can be adapted to specific needs by a broad range of
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223 parameters:
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224
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225 * *scoring* of the alignment, e.g. influencing the cost of
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226 insertions/deletions and the weight of sequence vs. structure
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227 similarity.
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228
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229 * *RNA folding*, which control the secondary RNA structure prediciton.
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230
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231 * *heuristics*, which trade alignment accuracy vs. computation
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232 speed. The huge complexity of simultaneous alignment and folding
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233 generally requires some heuristics for reasonable computation times.
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234 Some alignment instances and alignment modes will require relaxation
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235 of the default heuristics; in particular, local, constrained, and free end gap
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236 alignment, will often require turning off the "maximal difference for
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237 alignment traces" heuristic.
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238
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239 * *constraints*, which can be applied to include prior knowledge to
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240 improve the quality of results and/or speed of computation.
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241
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242 **Input.**
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243
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244 Input consists of two sequences or alignments, which are specified in
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245 fasta, clustal, stockholm, or LocARNA pp format.
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246
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247 Optionally, one can specify structure and anchor constraints in these
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248 input files.
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249
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250 **Output.**
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251
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252 The final pairwise alignment is reported in standard and/or variants of the
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253 clustal and stockholm format, as well as LocARNA's own pp format.
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254
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255 For more information, see
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256 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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257 ]]></help>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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258
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259 <expand macro="citations" />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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261 </tool>