Mercurial > repos > rnateam > locarna_pairwise

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 94c141a71ef115279f1090f782b6f5cdeea9c277
author bgruening
date Mon, 19 Aug 2024 18:52:50 +0000
parents f3f08a777c10
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1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>
1
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3 Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse)
0
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version" />
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11 <command><![CDATA[
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12 #if str($alignment_mode.alignment_mode_selector) == "sparse"
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13 sparse
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14 #else
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15 locarna
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16 #end if
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18 '$inputA'
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19 '$inputB'
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20
3
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21 ## --width 60
0
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22
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23 ## -------------------- alignment mode and specific options ----------------#
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24
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25 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
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26 #if str($alignment_mode.free_endgaps) != "----"
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27 --free-endgaps $alignment_mode.free_endgaps
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28 #end if
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29 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
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30 --sequ-local on
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31 #else if str($alignment_mode.alignment_mode_selector) == "structure_local_locarna"
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32 --struct-local on
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33 #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna"
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34 --sequ-local on
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35 --struct-local on
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36 #end if
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37
1
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38 @SCORING_ARGS@
0
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39
1
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40 @FOLDING_ARGS@
0
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41 $Folding.alifold_consensus_dp
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42 --consensus-structure $Folding.consensus_structure
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43
1
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44 @HEURISTIC_ARGS@
0
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45
2
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46 #if str($alignment_mode.alignment_mode_selector) == "sparse"
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47 @HEURISTIC_SPARSE_ARGS@
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48 #end if
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49
1
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50 @CONSTRAINT_ARGS@
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51
4
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52 ## -------------------- output ----------------#
0
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53
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54 #if 'stockholm' in str($outputs).split(",")
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55 --stockholm '$stockholm'
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56 #end if
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57 #if 'clustal' in str($outputs).split(",")
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58 --clustal '$clustal'
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59 #end if
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60 #if 'clustal_strict' in str($outputs).split(",") and (not 'clustal' in str($outputs).split(","))
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61 --clustal '$clustal_strict'
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62 #end if
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63 #if 'pp' in str($outputs).split(",")
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64 --pp '$pp'
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65 #end if
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66
1
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67 @STDOUT_ARGS@
0
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69 #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",")
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70 && cp $clustal $clustal_strict
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71 #end if
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73 #if 'clustal_strict' in str($outputs).split(",")
1
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74 && cp '$clustal_strict' '$clustal_strict~'
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75 && sed '/^#/d' '$clustal_strict~' >'$clustal_strict'
0
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76 #end if
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78 ]]></command>
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79
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80 <inputs>
4
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81 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
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82 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
0
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83 <conditional name="alignment_mode">
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84 <param name="alignment_mode_selector" type="select" label="Alignment mode" help="Note that local alignment mode usually requires to turn off the 'max-diff' heuristic (maximal difference for alignment traces).">
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85 <option value="global_locarna">Global alignment(LocARNA)</option>
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86 <option value="local_locarna">Local alignment (LocARNA)</option>
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87 <option value="sparse">Global fast alignment (SPARSE)</option>
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88 <option value="structure_sequence_local_locarna">Structure and sequence local alignment (LocARNA)</option>
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89 <option value="structure_local_locarna">Structure local, sequence global alignment (LocARNA)</option>
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90 </param>
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91 <when value="global_locarna">
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92 <param name="free_endgaps" type="select" label="Free endgaps" help="Specify whether gaps at the ends (all, 5', or 3' ends) of the sequences should be penalized or allowed for free.">
0
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93 <option value="----">None</option>
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94 <option value="++++">All</option>
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95 <option value="+-+-">5' ends</option>
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96 <option value="-+-+">3' ends</option>
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97 <option value="++--">first sequence</option>
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98 <option value="--++">second sequence</option>
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99 <option value="+---">sequence A, 5' end</option>
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100 <option value="-+--">sequence A, 3' end</option>
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101 <option value="--+-">sequence B, 5' end</option>
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102 <option value="---+">sequence B, 3' end</option>
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103 </param>
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104 </when>
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105 <when value="local_locarna">
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106 </when>
2
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107 <when value="sparse">
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108 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">
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109 <expand macro="common_heuristic_parameters_sparse" />
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110 </section>
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111 </when>
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112
0
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113 <when value="structure_sequence_local_locarna" />
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114 <when value="structure_local_locarna" />
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115 </conditional>
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116
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117 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
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118 <option value="clustal_strict" selected="true">Output alignment in ClustalW format</option>
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119 <option value="clustal" selected="false">Output alignment in constraint-annotated ClustalW format</option>
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120 <option value="stockholm" selected="false">Output alignment in Stockholm format</option>
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121 <option value="pp" selected="false">Output alignment in LocARNA's PP 2.0 format</option>
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122 </param>
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123
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124 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
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125 <option value="--quiet">Don't report standard output</option>
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126 <option value="">Non verbose</option>
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127 <option value="--verbose">Verbose</option>
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128 </param>
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129
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130 <section name="Scoring" title="Scoring parameters">
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131 <expand macro="common_scoring_parameters" />
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132 </section>
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133
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134 <section name="Folding" title="RNA folding parameters">
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135 <expand macro="common_folding_parameters" />
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136 <expand macro="alifold_consensus_parameter" />
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137 <param name="consensus_structure" type="select" label="Consensus structure type" help="Type of consensus structures written to screen and stockholm output">
0
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138 <!-- <option value="mea">mea</option>-->
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139 <option value="none">none</option>
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140 <option value="alifold">alifold</option>
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141 </param>
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142 </section>
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143
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144 <section name="Heuristics" title="Heuristic parameters">
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145 <expand macro="common_heuristic_parameters" />
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146 <expand macro="max_diff_parameters_aln" />
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147 </section>
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148
1
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149 <section name="Constraints" title="Constraint parameters">
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150 <expand macro="common_constraint_parameters" />
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151 </section>
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152 </inputs>
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153
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154 <outputs>
1
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155 <expand macro="standard_outupt" />
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156 <data format="clustal" name="clustal" label="${tool.name} on ${on_string}: alignment (annotated clustal)">
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157 <filter>'clustal' in outputs</filter>
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158 </data>
4
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159 <data format="clustal" name="clustal_strict" label="${tool.name}on ${on_string}: alignment (clustal)">
0
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160 <filter>'clustal_strict' in outputs</filter>
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161 </data>
4
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162 <data format="stockholm" name="stockholm" label="${tool.name} on ${on_string}: alignment (stockholm)">
0
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163 <filter>'stockholm' in outputs</filter>
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164 </data>
4
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165 <data format="txt" name="pp" label="${tool.name} on ${on_string}: alignment (PP 2.0)">
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166 <filter>'pp' in outputs</filter>
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167 </data>
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168 </outputs>
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169
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170 <tests>
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171 <test expect_num_outputs="1">
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172 <param name="inputA" value="tRNA_2-1.fa" />
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173 <param name="inputB" value="tRNA_2-2.fa" />
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174 <param name="outputs" value="clustal" />
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175 <output name="clustal" file="tRNA_2.aln" lines_diff="2" />
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176 </test>
3
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177 <test expect_num_outputs="2">
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178 <param name="inputA" value="haca.snoRNA-1.aln" />
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179 <param name="inputB" value="haca.snoRNA-2.aln" />
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180 <param name="outputs" value="clustal_strict,clustal" />
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181 <output name="clustal" file="haca.snoRNA-c.aln" lines_diff="2" />
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182 <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="2" />
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183 </test>
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184 </tests>
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185
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186 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs**
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187
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188 Pairwise RNA alignment tools of the LocARNA suite (locarna,
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189 sparse). These tools perform variants of simultaneous RNA folding and
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190 alignment. They can be adapted to specific needs by a broad range of
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191 parameters:
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192
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193 * *scoring* of the alignment, e.g. influencing the cost of
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194 insertions/deletions and the weight of sequence vs. structure
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195 similarity.
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196
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197 * *RNA folding*, which control the secondary RNA structure prediciton.
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198
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199 * *heuristics*, which trade alignment accuracy vs. computation
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200 speed. The huge complexity of simultaneous alignment and folding
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201 generally requires some heuristics for reasonable computation times.
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202 Some alignment instances and alignment modes will require relaxation
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203 of the default heuristics; in particular, local, constrained, and free end gap
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204 alignment, will often require turning off the "maximal difference for
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205 alignment traces" heuristic.
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206
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207 * *constraints*, which can be applied to include prior knowledge to
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208 improve the quality of results and/or speed of computation.
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209
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210 **Input.**
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211
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212 Input consists of two sequences or alignments, which are specified in
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213 fasta, clustal, stockholm, or LocARNA pp format.
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214
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215 Optionally, one can specify structure and anchor constraints in these
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216 input files.
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217
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218 **Output.**
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219
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220 The final pairwise alignment is reported in standard and/or variants of the
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221 clustal and stockholm format, as well as LocARNA's own pp format.
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222
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223 For more information, see
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224 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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225 ]]></help>
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226
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227 <expand macro="citations" />
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228
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229 </tool>