Mercurial > repos > rnateam > locarna_pairwise_p

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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 18:52:22 +0000
parents 535f2e41d4f7
children
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1 <tool id="locarna_pairwise_p" name="LocARNA Pairwise Probability Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 Partition Function and Probabilities from Pairwise Simultaneous Alignment and Folding of RNAs (LocARNA-P)
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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 locarna_p
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13 '$inputA'
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14 '$inputB'
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15
0
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16 @SCORING_ARGS@
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17
0
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18 @FOLDING_ARGS@
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20 @HEURISTIC_ARGS@
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21 #if float($Heuristics.pf_scale) != 1.0
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22 --pf-scale $Heuristics.pf_scale
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23 #end if
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24
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25 ## -------------------- other parameters ----------------#
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26 @CONSTRAINT_ARGS_WOLP@
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27
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28 ## -------------------- probability parameters ----------------#
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29 $Probabilities.include_am_in_bm
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30 #if float($Probabilities.min_bm_prob) != 0.0005
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31 --min-bm-prob $Probabilities.min_bm_prob
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32 #end if
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33 #if float($Probabilities.min_am_prob) != 0.0005
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34 --min-am-prob $Probabilities.min_am_prob
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35 #end if
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36
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37 ## -------------------- output ----------------#
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38
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39 #if not $arc_match_probs is None
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40 --write-arcmatch-probs=$arc_match_probs
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41 #end if
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42
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43 #if not $base_match_probs is None
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44 --write-basematch-probs=$base_match_probs
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45 #end if
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46
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47 @STDOUT_ARGS@
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48
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49 ]]></command>
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50
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51 <inputs>
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52 <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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53 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
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54 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
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55 <option value="base_match_probs" selected="true">Output base match probabilities</option>
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56 <option value="arc_match_probs" selected="true">Output arc match probabilities</option>
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57 </param>
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58 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
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59 <option value="--quiet">Don't report standard output</option>
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60 <option value="">Non verbose</option>
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61 <option value="--verbose">Verbose</option>
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62 </param>
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63 <section name="Probabilities" title="Probability parameters">
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64 <param argument="--include-am-in-bm" type="boolean" truevalue="--include-am-in-bm" falsevalue="" label="Include arc match cases in computation of base match probabilities" />
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65 <param argument="--min-bm-prob" type="float" value="0.0005" min="0.0" max="1.0" label="Minimal base match probability"/>
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66 <param argument="--min-am-prob" type="float" value="0.0005" min="0.0" max="1.0" label="Minimal arc match probability"/>
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67 </section>
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68
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69 <section name="Scoring" title="Scoring parameters">
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70 <expand macro="common_scoring_parameters" />
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71 </section>
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73 <section name="Folding" title="RNA folding parameters">
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74 <expand macro="common_folding_parameters" />
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75 </section>
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77 <section name="Heuristics" title="Heuristic parameters">
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78 <expand macro="common_heuristic_parameters" />
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79 <expand macro="max_diff_parameters_aln" />
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80 <param argument="--pf-scale" type="float" value="1.0" label="Scaling of the partition function." help="Use (only) if standard scaling overflows." />
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81 </section>
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83 <section name="Constraints" title="Constraint parameters">
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84 <expand macro="common_constraint_parameters_woLP" />
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85 </section>
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86 </inputs>
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87
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88 <outputs>
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89 <expand macro="standard_outupt" />
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90 <data format="table" name="base_match_probs" label="${tool.name} base match probabilties on ${on_string}">
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91 <filter>'base_match_probs' in outputs</filter>
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92 </data>
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93 <data format="table" name="arc_match_probs" label="${tool.name} arc match probabilties on ${on_string}">
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94 <filter>'arc_match_probs' in outputs</filter>
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95 </data>
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96 </outputs>
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97
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98 <tests>
2
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99 <test expect_num_outputs="2">
0
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100 <param name="inputA" value="tRNA_2-1.fa" />
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101 <param name="inputB" value="tRNA_2-2.fa" />
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102 <param name="outputs" value="arc_match_probs,base_match_probs"/>
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103 <param name="min_bm_prob" value="0.01" />
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104 <param name="min_am_prob" value="0.01" />
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105 <output name="base_match_probs" file="tRNA_2.bmprobs" />
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106 <output name="arc_match_probs" file="tRNA_2.amprobs" />
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107 </test>
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108 </tests>
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109
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110 <help><![CDATA[ **LocARNA -- Pairwise probability alignment of RNAs**
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111
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112 Pairwise probability alignment tool of the LocARNA suite. This tool
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113 computes base and arc match probabilities from simultaneous RNA
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114 folding and alignment. It can be adapted to specific needs by a broad
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115 range of parameters:
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116
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117 * *scoring* of the alignment, e.g. influencing the cost of
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118 insertions/deletions and the weight of sequence vs. structure
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119 similarity.
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120
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121 * *RNA folding*, which control the secondary RNA structure prediciton.
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122
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123 * *heuristics*, which trade alignment accuracy vs. computation
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124 speed. The huge complexity of simultaneous alignment and folding
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125 generally requires some heuristics for reasonable computation times.
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126 Some alignment instances and alignment modes will require relaxation
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127 of the default heuristics; in particular, local, constrained, and free end gap
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128 alignment, will often require turning off the "maximal difference for
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129 alignment traces" heuristic.
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130
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131 * *constraints*, which can be applied to include prior knowledge to
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132 improve the quality of results and/or speed of computation.
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133
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134 **Input.**
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135
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136 Input consists of two sequences or alignments, which are specified in
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137 fasta, clustal, stockholm, or LocARNA pp format.
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138
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139 Optionally, one can specify structure and anchor constraints in these
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140 input files.
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141
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142 **Output.**
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143
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144 The tool writes two tables of base match and arc match probabilities, respectively. Rows
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145 in the base match probabilities table consist of
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146
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147 i j p
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148
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149 where p is the probability of matching position i in the first sequence to position j in the second sequence.
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150
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151 For arc matchs, the table contains rows
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152
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153 i j k l p
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154
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155 where p is the probability of matching the base pair (i,j) of sequence one to (k,l) of sequence two.
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156
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157 Moreover, the partition function and further information can be written to standard out.
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158
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159 For more information, see
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160 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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161 ]]></help>
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162
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163 <expand macro="citations" />
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164
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165 </tool>