Mercurial > repos > bgruening > locarna_pairwise

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
author bgruening
date Wed, 28 Dec 2016 18:48:14 -0500
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b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.0">
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2 <description>
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3 Pairwise Simultaneous Alignment and Folding of RNAs
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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>
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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
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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 '$inputB'
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25
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26 --width 60
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27
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28 ## -------------------- alignment mode and specific options
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29
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30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
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31 #if str($alignment_mode.free_endgaps) != "----"
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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
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36 #else if str($alignment_mode.alignment_mode_selector) == "structure_local_locarna"
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37 --struct-local on
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38 #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna"
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39 --sequ-local on
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40 --struct-local on
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41 #end if
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42
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43 ## -------------------- scoring parameters
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44
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45 --indel $Scoring.indel
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46 --indel-opening $Scoring.indel_opening
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47 --struct-weight $Scoring.struct_weight
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48 --tau $Scoring.tau
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49
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50 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
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51 --match $Scoring.sequence_score.match
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52 --mismatch $Scoring.sequence_score.mismatch
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53 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
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54 --use-ribosum true
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55 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
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56 --ribofit true
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57 #end if
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58
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59 ## -------------------- folding parameters
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60
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61 #if float($Folding.rnafold_temperature) != 37.0
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62 --rnafold-temperature $Folding.rnafold_temperature
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63 #end if
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64
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65 $Folding.alifold_consensus_dp
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66 --consensus-structure $Folding.consensus_structure
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67
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68 ## -------------------- heuristic parameters
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69
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70 -p $Heuristics.min_prob
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71 --max-diff-am $Heuristics.max_diff_am
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72 --max-diff $Heuristics.max_diff
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73 --max-diff-at-am $Heuristics.max_diff_at_am
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74
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75 #if float($Heuristics.max_bps_length_ratio) != 0.0
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76 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
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77 #end if
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78
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79 ## -------------------- other parameters
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80
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81 $Constraint.lonely_pairs
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82
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83 #if $Constraint.maxBPspan != -1
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84 --maxBPspan $Constraint.maxBPspan
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85 #end if
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86
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87 $Constraint.ignore_constraints
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88
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89 ## -------------------- output
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90
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91 #if 'stockholm' in str($outputs).split(",")
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92 --stockholm '$stockholm'
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93 #end if
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94 #if 'clustal' in str($outputs).split(",")
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95 --clustal '$clustal'
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96 #end if
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97 #if 'clustal_strict' in str($outputs).split(",") and (not 'clustal' in str($outputs).split(","))
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98 --clustal '$clustal_strict'
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99 #end if
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100 #if 'pp' in str($outputs).split(",")
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101 --pp '$pp'
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102 #end if
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103
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104 $stdout_verbosity
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105
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106 #if str($stdout_verbosity) != "--quiet":
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107 > '$stdout'
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108 #end if
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109
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110 #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",")
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111 && cp $clustal $clustal_strict
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112 #end if
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113
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114 #if 'clustal_strict' in str($outputs).split(",")
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115 && sed -i '/\^#/d' '$clustal_strict'
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116 #end if
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117
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118 ]]></command>
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119
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120 <inputs>
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121 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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122 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
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123 />
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124 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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125 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
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126 />
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127 <conditional name="alignment_mode">
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128 <param name="alignment_mode_selector" type="select" label="Alignment mode"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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129 help="Note that local alignment mode usually requires to turn off
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130 the 'max-diff' heuristic (maximal difference for alignment traces)."
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131 >
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132 <option value="global_locarna">Global alignment
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133 (LocARNA)</option>
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134 <option value="local_locarna">Local alignment (LocARNA)</option>
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135 <option value="sparse">Global alignment (SPARSE)</option>
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136 <option value="structure_sequence_local_locarna">
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137 Structure and sequence local alignment (LocARNA)
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138 </option>
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139 <option value="structure_local_locarna">
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140 Structure local, sequence global alignment (LocARNA)
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141 </option>
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142 </param>
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143 <when value="global_locarna">
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144 <param name="free_endgaps" type="select" label="Free endgaps"
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145 help="Specify whether gaps at the ends (all, 5', or 3' ends)
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146 of the sequences should be penalized or allowed for free.">
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147 <option value="----">None</option>
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148 <option value="++++">All</option>
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149 <option value="+-+-">5' ends</option>
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150 <option value="-+-+">3' ends</option>
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151 <option value="++--">first sequence</option>
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152 <option value="--++">second sequence</option>
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153 <option value="+---">sequence A, 5' end</option>
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154 <option value="-+--">sequence A, 3' end</option>
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155 <option value="--+-">sequence B, 5' end</option>
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156 <option value="---+">sequence B, 3' end</option>
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157 </param>
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158 </when>
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159 <when value="local_locarna">
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160 </when>
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161 <when value="sparse" />
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162 <when value="structure_sequence_local_locarna" />
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163 <when value="structure_local_locarna" />
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164 </conditional>
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165
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166 <param name="outputs" type="select" display="checkboxes" multiple="True"
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167 label="Output options">
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168 <option value="clustal_strict" selected="True">Output alignment
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169 in ClustalW format</option>
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170 <option value="clustal" selected="False">Output alignment
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171 in constraint-annotated ClustalW format</option>
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172 <option value="stockholm" selected="False">Output
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173 alignment in Stockholm format</option>
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174 <option value="pp" selected="False">Output
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175 alignment in LocARNA's PP 2.0 format</option>
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176 </param>
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177
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178 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
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179 <option value="--quiet">Don't report standard
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180 output</option>
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181 <option value="">Non verbose</option>
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182 <option value="--verbose">Verbose</option>
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183 </param>
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184
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185 <section name="Scoring" title="Scoring parameters">
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186 <expand macro="common_scoring_parameters" />
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187 </section>
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188
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189 <section name="Folding" title="RNA folding parameters">
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190 <expand macro="common_folding_parameters" />
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191 <expand macro="alifold_consensus_parameter" />
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192 <param name="consensus_structure" type="select" label="Consensus structure type"
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193 help="Type of consensus structures written to screen and stockholm output"
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194 >
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195 <!-- <option value="mea">mea</option>-->
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196 <option value="none">none</option>
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197 <option value="alifold">alifold</option>
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198 </param>
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199 </section>
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200
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201 <section name="Heuristics" title="Heuristic parameters">
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202 <expand macro="common_heuristic_parameters" />
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203 </section>
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204
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205 <section name="Constraint" title="Constraint parameters">
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206 <expand macro="constraints" />
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207 </section>
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208 </inputs>
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209
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210 <outputs>
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211 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
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212 <filter>stdout_verbosity != '--quiet'</filter>
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213 </data>
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214 <data format="clustal" name="clustal"
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215 label="${tool.name} alignment (annotated clustal) on ${on_string}">
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216 <filter>'clustal' in outputs</filter>
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217 </data>
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218 <data format="clustal" name="clustal_strict"
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219 label="${tool.name} alignment (clustal) on ${on_string}">
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220 <filter>'clustal_strict' in outputs</filter>
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221 </data>
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222 <data format="stockholm" name="stockholm"
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223 label="${tool.name} alignment (stockholm) on ${on_string}">
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224 <filter>'stockholm' in outputs</filter>
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225 </data>
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226 <data format="txt" name="pp"
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227 label="${tool.name} alignment (PP 2.0) on ${on_string}">
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228 <filter>'pp' in outputs</filter>
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229 </data>
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230 </outputs>
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231
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232 <tests>
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233 <test>
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234 <param name="inputA" value="tRNA_2-1.fa" />
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235 <param name="inputB" value="tRNA_2-2.fa" />
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236 <param name="outputs" value="clustal" />
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237 <output name="clustal" file="tRNA_2.aln" />
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238 </test>
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239 </tests>
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240
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241 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs**
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242
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243 Pairwise RNA alignment tools of the LocARNA suite (locarna,
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244 sparse). These tools perform variants of simultaneous RNA folding and
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245 alignment. They can be adapted to specific needs by a broad range of
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246 parameters:
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247
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248 * *scoring* of the alignment, e.g. influencing the cost of
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249 insertions/deletions and the weight of sequence vs. structure
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250 similarity.
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251
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252 * *RNA folding*, which control the secondary RNA structure prediciton.
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253
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254 * *heuristics*, which trade alignment accuracy vs. computation
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255 speed. The huge complexity of simultaneous alignment and folding
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256 generally requires some heuristics for reasonable computation times.
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257 Some alignment instances and alignment modes will require relaxation
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258 of the default heuristics; in particular, local, constrained, and free end gap
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259 alignment, will often require turning off the "maximal difference for
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260 alignment traces" heuristic.
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261
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262 * *constraints*, which can be applied to include prior knowledge to
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263 improve the quality of results and/or speed of computation.
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264
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265 **Input.**
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266
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267 Input consists of two sequences or alignments, which are specified in
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268 fasta, clustal, stockholm, or LocARNA pp format.
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269
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270 Optionally, one can specify structure and anchor constraints in these
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271 input files.
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272
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273 **Output.**
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274
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275 The final pairwise alignment is reported in standard and/or variants of the
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276 clustal and stockholm format, as well as LocARNA's own pp format.
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277
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278 For more information, see
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279 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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280 ]]></help>
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281
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282 <expand macro="citations" />
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283
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284 </tool>