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annotate macros.xml @ 2:e66514da3a99 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 13:58:16 +0000
parents 8723e3f8e422
children a80f279b4ad0
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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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1 <macros>
2
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2 <token name="@TOOL_VERSION@">1.9.2.3</token>
e66514da3a99 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
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3 <token name="@VERSION_SUFFIX@">1</token>
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4 <token name="@PROFILE@">21.09</token>
0
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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 <xml name="requirements">
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">locarna</requirement>
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9 <requirement type="package" version="4.2.2">r-base</requirement>
0
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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10 </requirements>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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11 </xml>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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12
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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13 <xml name="stdio">
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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14 <stdio>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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15 <exit_code range="1:" />
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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16 </stdio>
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17 </xml>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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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 <xml name="version">
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20 <version_command>
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21 <![CDATA[
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22 mlocarna --version
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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 </version_command>
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25 </xml>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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26
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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27 <xml name="bed_anchors">
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28 <conditional name="bed_anchors">
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29 <param name="bed_anchors_selector" type="select" label="Anchor constraints"
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30 help="Anchor constraints in bed format specify positions of
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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31 named anchor regions per sequence. The sequence names
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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32 ('contig' names have to correspond to the fasta input
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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33 sequence names. Anchor names must be unique per sequence
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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34 and regions of the same name for different sequences
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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35 must have the same length. This constrains the alignment
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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36 to align all regions of the same name.">
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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37 <option value="no">Don't load anchor constraints from
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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38 bed file</option>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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39 <option value="yes">Load anchor constraints from bed
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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40 file</option>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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41 </param>
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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42 <when value="no" />
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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43 <when value="yes">
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44 <param name="bed_anchors_file" type="data" format="tabular"
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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45 label="Anchor constraint specification in bed format"
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46 />
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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47 </when>
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48 </conditional>
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49 </xml>
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50
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51 <xml name="common_scoring_parameters">
2
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52 <param argument="--struct-weight"
0
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53 label="Structure weight" type="integer"
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54 value="200" min="0" max="800" />
2
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55 <param argument="--indel-opening"
0
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56 label="Indel opening score" type="integer"
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57 value="-500" max="0" min="-1500" />
2
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58 <param argument="--indel" label="Indel score" type="integer"
0
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59 value="-350" min="-1000" max="0" />
2
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60 <param argument="--tau" type="integer" value="50"
0
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61 min="0" max="200"
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62 label="Sequence contribution at structure match in percent"/>
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63
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64 <conditional name="sequence_score">
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65 <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">
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66 <option value="ribofit">Use ribofit</option>
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67 <option value="ribosum">Use RIBOSUM85_60</option>
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68 <option value="match">Simple match/mismatch costs</option>
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69 </param>
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70 <when value="ribofit" />
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71 <when value="ribosum" />
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72 <when value="match">
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73 <param name="match" type="integer" value="50"
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74 min="0" max="400"
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75 label="Match score" />
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76 <param name="mismatch" type="integer" value="0"
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77 min="-400" max="0"
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78 label="Mismatch score" />
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79 </when>
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80 </conditional>
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81 </xml>
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82
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83 <xml name="plfolding_parameters">
2
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84 <param argument="--plfold-span"
0
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85 type="integer" value="150" min="-1" max="400"
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86 label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
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87
2
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88 <param argument="--plfold-winsize"
0
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89 type="integer" value="300" min="-1" max="800"
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90 label="Window size for local folding" />
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91 </xml>
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92
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93 <xml name="common_folding_parameters">
2
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94 <param argument="rnafold-temperature"
0
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95 type="float" value="37.0" min="10" max="50"
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96 label="Temperature for RNAfold (RNAfold's -T option)" />
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97 </xml>
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98
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99 <token name="@SCORING_ARGS@">
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100 ## -------------------- scoring parameters
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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101 --indel $Scoring.indel
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102 --indel-opening $Scoring.indel_opening
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103 --struct-weight $Scoring.struct_weight
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104 --tau $Scoring.tau
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105
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106 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
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107 --match $Scoring.sequence_score.match
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108 --mismatch $Scoring.sequence_score.mismatch
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109 #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
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110 --use-ribosum true
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111 #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
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112 --ribofit true
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113 #end if
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114 </token>
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115
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116 <token name="@FOLDING_ARGS@">
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117 ## -------------------- folding parameters
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118 #if float($Folding.rnafold_temperature) != 37.0
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119 --rnafold-temperature $Folding.rnafold_temperature
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120 #end if
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121 </token>
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122
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123 <token name="@HEURISTIC_ARGS@">
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124 ## -------------------- heuristic parameters
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125 -p $Heuristics.min_prob
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126
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127 #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off"
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128 --max-diff -1
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129 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff"
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130 --max-diff $Heuristics.max_diff_mode.max_diff
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131 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am"
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132 --max-diff -1
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133 --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am
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134 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln"
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135 --max-diff $Heuristics.max_diff_mode.max_diff
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136 --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln'
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137 $Heuristics.max_diff_mode.max_diff_relax
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138 #end if
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139
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140 --max-diff-am $Heuristics.max_diff_am
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141
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142 #if float($Heuristics.max_bps_length_ratio) > 0.0
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143 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
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144 #end if
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145 </token>
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146
1
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147 <token name="@HEURISTIC_SPARSE_ARGS@">
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148 --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold
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149 --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold
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150
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151 </token>
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152
2
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153 <token name="@CONSTRAINT_ARGS_WOLP@">
0
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154 #if $Constraints.maxBPspan != -1
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155 --maxBPspan $Constraints.maxBPspan
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156 #end if
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157
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158 $Constraints.ignore_constraints
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159 </token>
2
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160 <token name="@CONSTRAINT_ARGS@">
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161 ## -------------------- constraint parameters
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162 $Constraints.lonely_pairs
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163 @CONSTRAINT_ARGS_WOLP@
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164 </token>
0
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165
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166 <token name="@STDOUT_ARGS@">
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167 $stdout_verbosity
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168
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169 #if str($stdout_verbosity) != "--quiet":
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170 > '$stdout'
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171 #end if
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172 </token>
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173
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174 <xml name="max_diff_parameters_selector">
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175 <param name="max_diff_mode_selector" type="select"
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176 label="Restrict alignable positions by maximum difference"
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177 help="(max-diff*)">
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178 <option value="off">Off</option>
2
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179 <option value="max-diff" selected="true">Maximal difference of aligned positions</option>
0
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180 <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option>
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181 <yield />
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182 </param>
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183 </xml>
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184
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185 <xml name="max_diff_parameters_standard_cases">
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186 <when value="off" />
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187 <when value="max-diff">
2
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188 <param argument="--max-diff" type="integer"
0
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189 value="60" min="-1" max="300"
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190 label="Maximal difference of aligned positions" />
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191 </when>
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192 <when value="max-diff-at-am">
2
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193 <param argument="--max-diff-at-am" type="integer"
0
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194 value="60" min="-1" max="300"
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195 label="Maximal difference of aligned positions,
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196 only at arc match positions" />
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197 </when>
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198 </xml>
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199
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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200 <xml name="max_diff_parameters">
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201 <conditional name="max_diff_mode">
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202 <expand macro="max_diff_parameters_selector" />
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203 <expand macro="max_diff_parameters_standard_cases" />
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204 </conditional>
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205 </xml>
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206
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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207 <xml name="max_diff_parameters_aln">
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208 <conditional name="max_diff_mode">
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209 <expand macro="max_diff_parameters_selector">
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210 <option value="max-diff-aln">Maximal difference to a reference alignment</option>
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211 </expand>
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212 <expand macro="max_diff_parameters_standard_cases" />
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213 <when value="max-diff-aln">
2
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214 <param argument="--max-diff-aln" type="data" format="clustal"
0
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215 label="Reference alignment"
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216 />
2
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217 <param argument="--max-diff" type="integer"
0
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218 value="60" min="-1" max="300"
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219 label="Maximal difference of aligned positions" />
2
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220 <param argument="--max-diff-relax" type="boolean"
0
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221 truevalue="--max-diff-relax" falsevalue=""
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222 checked="False"
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223 label="Relax deviation constraints in multiple
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224 aligmnent."
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225 />
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226 </when>
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227 </conditional>
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228 </xml>
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229
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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230 <xml name="common_heuristic_parameters">
2
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231 <param argument="--min-prob" type="float" value="0.0005"
0
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232 min="0.0" max="0.2"
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233 label="Minimal / cutoff probability" />
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234
2
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235 <param argument="--max-diff-am"
0
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236 type="integer" value="30"
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237 min="-1" max="300"
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238 label="Maximal difference for sizes of matched arcs (-1=off)" />
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239
2
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240 <param argument="--max-bps-length-ratio"
0
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241 type="float" value="0.0" min="0.0" max="10.0"
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242 label="Maximal ratio 'number of considered base pairs' by
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243 'sequence length' (default: 0.0 = no effect)" />
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244 </xml>
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245
1
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246 <xml name="common_heuristic_parameters_sparse">
2
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247 <param argument="--prob-unpaired-in-loop-threshold" type="float" value="0.00005"
1
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248 min="0.0" max="0.2"
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249 label="Probability threshold for unpaired bases in loops" />
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250
2
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251 <param argument="--prob-basepair-in-loop-threshold" type="float" value="0.0001"
1
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252 min="0.0" max="0.2"
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253 label="Probability threshold for base pairs in loops" />
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254 </xml>
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255
0
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256 <xml name="in_loop_ratio_parameters">
2
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257 <param argument="--max-uil-length-ratio"
0
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258 type="float" value="0.0" min="0.0" max="10.0"
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259 label="Maximal ratio 'number considered unpaired bases in loops' by
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260 'sequence length' (default: 0.0; no effect)" />
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261
2
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262 <param argument="--max-bpil-length-ratio"
0
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263 type="float" value="0.0" min="0.0" max="10.0"
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264 label="Maximal ratio 'number of considered base pairs in loops'
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265 by 'sequence length' (default: 0.0; no effect)" />
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266 </xml>
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267
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268 <xml name="exparnap_in_loop_parameters">
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269 <param argument="--prob_unpaired_in_loop_threshold"
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270 type="float" value="0.01" min="0.0" max="1.0"
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271 label="Probability threshold for unpaired bases in loops" />
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272 <param argument="--prob_basepair_in_loop_threshold"
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273 type="float" value="0.01" min="0.0" max="1.0"
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274 label="Probability threshold for base pairs in loops" />
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275 </xml>
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276
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277 <xml name="alifold_consensus_parameter">
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278 <param argument="--alifold-consensus-dp"
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279 type="boolean" checked="False"
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280 truevalue="--alifold-consensus-dp" falsevalue=""
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281 label="Compute consensus dot plot by alifold" />
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282 </xml>
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283
2
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284 <xml name="common_constraint_parameters_woLP">
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285 <yield/>
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286 <param argument="--maxBPspan"
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287 type="integer" value="-1" min="-1" max="400"
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288 label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
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289 <param argument="--ignore-constraints"
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290 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
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291 help="Ignore all anchor and structure constraints given
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292 in the fasta(-ish) input." />
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293 </xml>
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294
2
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295 <xml name="common_constraint_parameters">
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296 <expand macro="common_constraint_parameters_woLP">
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297 <param argument="--noLP" name="lonely_pairs" type="boolean" truevalue="" falsevalue="--noLP"
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298 checked="true" label="Allow lonely base-pairs"/>
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299 </expand>
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300 </xml>
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301
0
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302 <xml name="standard_outupt">
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303 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout">
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304 <filter>stdout_verbosity != '--quiet'</filter>
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305 </data>
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306 </xml>
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307
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308 <xml name="mlocarna_outputs">
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309 <expand macro="standard_outupt" />
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310 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
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311 label="${tool.name} on ${on_string}: alignment (annotated clustal)">
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312 <filter>'clustal' in outputs</filter>
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313 </data>
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314 <data format="clustal" name="clustal_strict"
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315 from_work_dir="mlocarna_results/results/result.strict-aln"
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316 label="${tool.name} on ${on_string}: alignment (clustal)">
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317 <filter>'strict' in outputs</filter>
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318 </data>
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319 <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
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320 label="${tool.name} on ${on_string}: alignment (stockholm)">
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321 <filter>'stockholm' in outputs</filter>
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322 </data>
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323 <data format="txt" name="pp"
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324 from_work_dir="mlocarna_results/results/result.pp"
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325 label="${tool.name} on ${on_string}: alignment (PP 2.0)">
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326 <filter>'pp' in outputs</filter>
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327 </data>
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328 <data format="tar.gz" name="mlocarna_results_tgz"
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329 label="${tool.name} on ${on_string}: results archive">
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330 <filter>'mlocarna_results' in outputs</filter>
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331 </data>
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332 </xml>
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333
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334 <xml name="citations">
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335 <citations>
1
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336 <citation type="doi">10.1371/journal.pcbi.0030065</citation>
0
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337 <citation type="doi">10.1261/rna.029041.111</citation>
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338 <citation type="doi">10.1093/bioinformatics/btv185</citation>
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339 <citation type="doi">10.1186/s12859-014-0404-0</citation>
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340 </citations>
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341 </xml>
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342 </macros>
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343