Mercurial > repos > rnateam > locarna_reliability_profile

annotate macros.xml @ 2:dd991ca3d8ce draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author rnateam
date Sat, 21 Jan 2017 17:38:37 -0500
parents 9942e1b7646c
children e84d1fc87829
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7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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1 <macros>
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2 <token name="@VERSION@">1.9.0</token>
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3
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">locarna</requirement>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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7 </requirements>
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8 </xml>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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9
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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10 <xml name="stdio">
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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14 </xml>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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15
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16 <xml name="version">
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17 <version_command>
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18 <![CDATA[
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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19 mlocarna --version
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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20 ]]>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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21 </version_command>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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22 </xml>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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23
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24 <xml name="bed_anchors">
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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25 <conditional name="bed_anchors">
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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26 <param name="bed_anchors_selector" type="select" label="Anchor constraints"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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27 help="Anchor constraints in bed format specify positions of
1
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28 named anchor regions per sequence. The sequence names
9942e1b7646c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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29 ('contig' names have to correspond to the fasta input
9942e1b7646c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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30 sequence names. Anchor names must be unique per sequence
9942e1b7646c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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31 and regions of the same name for different sequences
9942e1b7646c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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32 must have the same length. This constrains the alignment
9942e1b7646c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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33 to align all regions of the same name.">
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34 <option value="no">Don't load anchor constraints from
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35 bed file</option>
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36 <option value="yes">Load anchor constraints from bed
9942e1b7646c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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37 file</option>
0
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38 </param>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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39 <when value="no" />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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40 <when value="yes">
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41 <param name="bed_anchors_file" type="data" format="tabular"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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42 label="Anchor constraint specification in bed format"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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43 />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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44 </when>
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45 </conditional>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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46 </xml>
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47
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48 <xml name="common_scoring_parameters">
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49 <param name="struct_weight" argument="struct-weight"
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50 label="Structure weight" type="integer"
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51 value="200" min="0" max="800" />
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52 <param name="indel_opening" argument="indel-opening"
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53 label="Indel opening score" type="integer"
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54 value="-500" max="0" min="-1500" />
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55 <param argument="indel" label="Indel score" type="integer"
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56 value="-350" min="-1000" max="0" />
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57 <param argument="tau" type="integer" value="50"
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58 min="0" max="200"
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59 label="Sequence contribution at structure match in percent"/>
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60
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61 <conditional name="sequence_score">
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62 <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">
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63 <option value="ribofit">Use ribofit</option>
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64 <option value="ribosum">Use RIBOSUM85_60</option>
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65 <option value="match">Simple match/mismatch costs</option>
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66 </param>
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67 <when value="ribofit" />
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68 <when value="ribosum" />
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69 <when value="match">
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70 <param name="match" type="integer" value="50"
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71 min="0" max="400"
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72 label="Match score" />
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73 <param name="mismatch" type="integer" value="0"
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74 min="-400" max="0"
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75 label="Mismatch score" />
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76 </when>
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77 </conditional>
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78 </xml>
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79
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80 <xml name="plfolding_parameters">
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81 <param name="plfold_span" argument="--plfold-span"
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82 type="integer" value="150" min="-1" max="400"
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83 label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
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84
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85 <param name="plfold_winsize" argument="--plfold-winsize"
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86 type="integer" value="300" min="-1" max="800"
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87 label="Window size for local folding" />
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88 </xml>
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89
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90 <xml name="common_folding_parameters">
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91 <param name="rnafold_temperature" argument="rnafold-temperature"
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92 type="float" value="37.0" min="10" max="50"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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93 label="Temperature for RNAfold (RNAfold's -T option)" />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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94 </xml>
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95
1
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96 <token name="@SCORING_ARGS@">
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97 ## -------------------- scoring parameters
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98 --indel $Scoring.indel
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99 --indel-opening $Scoring.indel_opening
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100 --struct-weight $Scoring.struct_weight
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101 --tau $Scoring.tau
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102
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103 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
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104 --match $Scoring.sequence_score.match
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105 --mismatch $Scoring.sequence_score.mismatch
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106 #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
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107 --use-ribosum true
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108 #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
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109 --ribofit true
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110 #end if
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111 </token>
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112
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113 <token name="@FOLDING_ARGS@">
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114 ## -------------------- folding parameters
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115 #if float($Folding.rnafold_temperature) != 37.0
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116 --rnafold-temperature $Folding.rnafold_temperature
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117 #end if
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118 </token>
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119
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120 <token name="@HEURISTIC_ARGS@">
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121 ## -------------------- heuristic parameters
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122 -p $Heuristics.min_prob
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123
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124 #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off"
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125 --max-diff -1
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126 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff"
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127 --max-diff $Heuristics.max_diff_mode.max_diff
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128 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am"
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129 --max-diff -1
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130 --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am
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131 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln"
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132 --max-diff $Heuristics.max_diff_mode.max_diff
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133 --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln'
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134 $Heuristics.max_diff_mode.max_diff_relax
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135 #end if
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136
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137 --max-diff-am $Heuristics.max_diff_am
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138
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139 #if float($Heuristics.max_bps_length_ratio) > 0.0
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140 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
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141 #end if
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142 </token>
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143
2
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144 <token name="@HEURISTIC_SPARSE_ARGS@">
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145 --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold
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146 --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold
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147
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148 </token>
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149
1
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150 <token name="@CONSTRAINT_ARGS@">
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151 ## -------------------- constraint parameters
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152 $Constraints.lonely_pairs
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153
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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>
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160
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161 <token name="@STDOUT_ARGS@">
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162 $stdout_verbosity
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163
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164 #if str($stdout_verbosity) != "--quiet":
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165 > '$stdout'
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166 #end if
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167 </token>
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168
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169 <xml name="max_diff_parameters_selector">
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170 <param name="max_diff_mode_selector" type="select"
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171 label="Restrict alignable positions by maximum difference"
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172 help="(max-diff*)">
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173 <option value="off">Off</option>
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174 <option value="max-diff" selected="True">Maximal difference of aligned positions</option>
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175 <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option>
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176 <yield />
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177 </param>
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178 </xml>
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179
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180 <xml name="max_diff_parameters_standard_cases">
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181 <when value="off" />
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182 <when value="max-diff">
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183 <param name="max_diff" argument="max-diff" type="integer"
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184 value="60" min="-1" max="300"
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185 label="Maximal difference of aligned positions" />
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186 </when>
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187 <when value="max-diff-at-am">
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188 <param name="max_diff_at_am" argument="max-diff-at-am" type="integer"
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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 only at arc match positions" />
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192 </when>
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193 </xml>
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194
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195 <xml name="max_diff_parameters">
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196 <conditional name="max_diff_mode">
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197 <expand macro="max_diff_parameters_selector" />
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198 <expand macro="max_diff_parameters_standard_cases" />
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199 </conditional>
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200 </xml>
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201
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202 <xml name="max_diff_parameters_aln">
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203 <conditional name="max_diff_mode">
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204 <expand macro="max_diff_parameters_selector">
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205 <option value="max-diff-aln">Maximal difference to a reference alignment</option>
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206 </expand>
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207 <expand macro="max_diff_parameters_standard_cases" />
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208 <when value="max-diff-aln">
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209 <param name="max_diff_aln" argument="max-diff-aln" type="data" format="clustal"
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210 label="Reference alignment"
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211 />
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212 <param name="max_diff" argument="max-diff" type="integer"
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213 value="60" min="-1" max="300"
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214 label="Maximal difference of aligned positions" />
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215 <param name="max_diff_relax" argument="max-diff-relax" type="boolean"
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216 truevalue="--max-diff-relax" falsevalue=""
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217 checked="False"
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218 label="Relax deviation constraints in multiple
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219 aligmnent."
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220 />
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221 </when>
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222 </conditional>
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223 </xml>
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224
0
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225 <xml name="common_heuristic_parameters">
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226 <param name="min_prob" argument="min-prob" type="float" value="0.0005"
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227 min="0.0" max="0.2"
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228 label="Minimal / cutoff probability" />
1
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229
0
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230 <param name="max_diff_am" argument="max-diff-am"
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231 type="integer" value="30"
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232 min="-1" max="300"
1
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233 label="Maximal difference for sizes of matched arcs (-1=off)" />
0
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234
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235 <param name="max_bps_length_ratio" argument="max-bps-length-ratio"
1
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236 type="float" value="0.0" min="0.0" max="10.0"
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237 label="Maximal ratio 'number of considered base pairs' by
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238 'sequence length' (default: 0.0 = no effect)" />
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239 </xml>
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240
2
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241 <xml name="common_heuristic_parameters_sparse">
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242 <param name="prob_unpaired_in_loop_threshold" argument="prob-unpaired-in-loop-threshold" type="float" value="0.00005"
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243 min="0.0" max="0.2"
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244 label="Probability threshold for unpaired bases in loops" />
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245
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246 <param name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001"
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247 min="0.0" max="0.2"
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248 label="Probability threshold for base pairs in loops" />
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249 </xml>
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250
1
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251 <xml name="in_loop_ratio_parameters">
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252 <param name="max_uil_length_ratio" argument="max-uil-length-ratio"
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253 type="float" value="0.0" min="0.0" max="10.0"
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254 label="Maximal ratio 'number considered unpaired bases in loops' by
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255 'sequence length' (default: 0.0; no effect)" />
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256
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257 <param name="max_bpil_length_ratio" argument="max-bpil-length-ratio"
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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 of considered base pairs in loops'
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260 by 'sequence length' (default: 0.0; no effect)" />
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261 </xml>
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262
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263 <xml name="exparnap_in_loop_parameters">
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264 <param name="prob_unpaired_in_loop_threshold"
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265 argument="prob_unpaired_in_loop_threshold"
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266 type="float" value="0.01" min="0.0" max="1.0"
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267 label="Probability threshold for unpaired bases in loops" />
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268 <param name="prob_basepair_in_loop_threshold"
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269 argument="prob_basepair_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 base pairs in loops" />
0
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272 </xml>
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273
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274 <xml name="alifold_consensus_parameter">
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275 <param name="alifold_consensus_dp" argument="alifold-consensus-dp"
1
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276 type="boolean" checked="False"
0
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277 truevalue="--alifold-consensus-dp" falsevalue=""
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278 label="Compute consensus dot plot by alifold" />
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279 </xml>
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280
1
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281 <xml name="common_constraint_parameters">
0
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282 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP"
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283 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
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284 <param name="maxBPspan" argument="--maxBPspan"
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285 type="integer" value="-1" min="-1" max="400"
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286 label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
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287 <param name="ignore_constraints" argument="ignore-constraints"
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288 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
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289 help="Ignore all anchor and structure constraints given
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290 in the fasta(-ish) input." />
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291 </xml>
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292
1
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293 <xml name="standard_outupt">
0
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294 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
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295 <filter>stdout_verbosity != '--quiet'</filter>
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296 </data>
1
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297 </xml>
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298
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299 <xml name="mlocarna_outputs">
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300 <expand macro="standard_outupt" />
0
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301 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
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302 label="${tool.name} alignment (annotated clustal) on ${on_string}">
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303 <filter>'clustal' in outputs</filter>
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304 </data>
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305 <data format="clustal" name="clustal_strict"
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306 from_work_dir="mlocarna_results/results/result.strict-aln"
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307 label="${tool.name} alignment (clustal) on ${on_string}">
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308 <filter>'clustal_strict' in outputs</filter>
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309 </data>
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310 <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
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311 label="${tool.name} alignment (stockholm) on ${on_string}">
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312 <filter>'stockholm' in outputs</filter>
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313 </data>
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314 <data format="txt" name="pp"
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315 from_work_dir="mlocarna_results/results/result.pp"
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316 label="${tool.name} alignment (PP 2.0) on ${on_string}">
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317 <filter>'pp' in outputs</filter>
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318 </data>
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319 <data format="tar.gz" name="mlocarna_results_tgz"
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320 label="${tool.name} results archive on ${on_string}">
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321 <filter>'mlocarna_results' in outputs</filter>
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322 </data>
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323 </xml>
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324
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325 <xml name="citations">
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326 <citations>
2
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327 <citation type="doi">10.1371/journal.pcbi.0030065</citation>
0
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328 <citation type="doi">10.1261/rna.029041.111</citation>
1
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329 <citation type="doi">10.1093/bioinformatics/btv185</citation>
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330 <citation type="doi">10.1186/s12859-014-0404-0</citation>
0
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331 </citations>
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332 </xml>
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333
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334
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335
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336 </macros>
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337