Mercurial > repos > rnateam > locarna_exparnap

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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 18:53:00 +0000
parents e66514da3a99
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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e66514da3a99 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
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1 <tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>
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3 Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-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"/>
0
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11 <command><![CDATA[
e91e4f48875e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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12 exparna_p
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13 '$inputA'
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14 '$inputB'
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15
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16 ## -------------------- scoring parameters -------------#
0
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17 $Scoring.no_stacking
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18 --alpha_1 $Scoring.alpha_1
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19 --alpha_2 $Scoring.alpha_2
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20 --alpha_3 $Scoring.alpha_3
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21 --struct-mismatch-score $Scoring.struct_mismatch_score
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23 @HEURISTIC_ARGS@
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24 --max-uil-length-ratio $Heuristics.max_uil_length_ratio
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25 --max-bpil-length-ratio $Heuristics.max_bpil_length_ratio
0
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26 --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
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27 --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold
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28
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29 @CONSTRAINT_ARGS@
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30 @FOLDING_ARGS@
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31 ## -------------------- other parameters---------------- #
0
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32 #if str($Other.subopt.subopt_selector) == "on"
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33 --diff-to-opt-score $Other.subopt.diff_to_opt_score
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34 --number-of-EPMs $Other.subopt.number_of_EPMs
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35 #end if
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36
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37 --min-score $Other.min_score
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38
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39 $Other.inexact_struct_match
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40 $Other.add_filter
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41 $Other.no_chaining
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42 --out-min-prob $Other.out_min_prob
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43
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44 ## -------------------- output ---------------- #
0
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45
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46 #if 'postscript' in str($outputs).split(",")
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47 --output-ps
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48 --PS_fileA '$ps_fileA'
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49 --PS_fileB '$ps_fileB'
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50 #end if
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51
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52 #if 'anchors-fasta' in str($outputs).split(",")
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53 --output-locarna '$anchors_fasta'
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54 #end if
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55
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56 #if 'anchors-pp' in str($outputs).split(",")
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57 --output-anchor-pp anchors_pp
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58 #end if
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59
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60 #if 'clustal' in str($outputs).split(",")
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61 --output-clustal '$clustal'
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62 #end if
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63
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64 #if 'epm_list' in str($outputs).split(",")
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65 --output-epm-list '$epm_list'
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66 #end if
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67
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68 #if 'chained_epm_list' in str($outputs).split(",")
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69 --output-chained-epm-list '$chained_epm_list'
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70 #end if
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72 @STDOUT_ARGS@
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73
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74 ## -------------------- post processing --------------#
0
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75
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76 #if 'anchors-pp' in str($outputs).split(",")
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77 && mv anchors_pp_A.pp '$anchors_ppA'
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78 && mv anchors_pp_B.pp '$anchors_ppB'
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79 #end if
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80
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81 ]]></command>
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82
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83 <inputs>
3
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84 <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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85 <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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86 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
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87 <option value="postscript" selected="false">Best EPM chain as colored postscript</option>
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88 <option value="anchors-fasta" selected="false">Fasta with anchor constraints from chaining</option>
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89 <option value="anchors-pp" selected="false">LocARNA PP files merging input PPs and anchor constraints from chaining</option>
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90 <option value="clustal" selected="false">Chain as alignment in Clustal format</option>
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91 <option value="epm_list" selected="false">List of the found EPMs</option>
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92 <option value="chained_epm_list" selected="false">List of EPMs in the best chain</option>
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93 </param>
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94 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
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95 <option value="--quiet">Don't report standard output</option>
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96 <option value="" selected="true">Non verbose</option>
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97 <option value="--verbose">Verbose</option>
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98 </param>
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99 <section name="Scoring" title="Scoring parameters">
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100 <param argument="--alpha_1" type="integer" value="1" min="0" max="50" label="Sequence score factor"/>
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101 <param argument="--alpha_2" type="integer" value="5" min="0" max="50" label="Structure score factor"/>
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102 <param argument="--no-stacking" type="boolean" truevalue="" falsevalue="--no-stacking" label="Add stacking terms"/>
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103 <param argument="--alpha_3" type="integer" value="5" min="0" max="50" label="Stacking score factor"/>
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104 <param argument="--struct-mismatch-score" type="integer" value="-10" min="-100" max="0" label="Score for nucleotide mismatch in base pair match"/>
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105 </section>
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106 <section name="Folding" title="RNA folding parameters">
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107 <expand macro="common_folding_parameters" />
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108 </section>
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109 <section name="Heuristics" title="Heuristic parameters">
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110 <expand macro="common_heuristic_parameters" />
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111 <expand macro="max_diff_parameters" />
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112 <expand macro="in_loop_ratio_parameters" />
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113 <expand macro="exparnap_in_loop_parameters" />
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114 </section>
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115 <section name="Constraints" title="Constraint parameters">
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116 <expand macro="common_constraint_parameters" />
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117 </section>
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118 <section name="Other" title="Other parameters">
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119 <conditional name="subopt">
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120 <param name="subopt_selector" type="select" label="Suboptimal traceback of EPMs (exact pattern matches)" help="(--subopt)">
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121 <option value="off">Enumerate only optimal EPMs</option>
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122 <option value="on">Perform suboptimal traceback of EPMs</option>
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123 </param>
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124 <when value="off" />
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125 <when value="on">
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126 <param argument="--diff-to-opt-score" type="integer" value="-1" min="-20" max="0" label="Maximum score difference to optimum" />
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127 <param argument="--number-of-EPMs" type="integer" value="100" min="1" max="10000" label="Maximal number of EPMs" />
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128 </when>
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129 </conditional>
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130
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131 <param argument="--min-score" type="integer" value="30" min="0" max="1000" label="Minimum score of EPM" />
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132 <param argument="--inexact-struct-match" type="boolean" truevalue="--inexact-struct-match" falsevalue="" label="Allow inexact structure matches"/>
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133 <param argument="--add-filter" type="boolean" truevalue="--add-filter" falsevalue="" checked="false" label="Apply an additional filter to enumerate only EPMs that are maximally extended (only inexact)"/>
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134 <param argument="--no-chaining" type="boolean" truevalue="" falsevalue="--no-chaining" checked="true" label="Find best overall chain by chaining"/>
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135 <param argument="--out-min-prob" type="float" value="0.0005" min="0" max="1" label="Minimal probability in output (min-prob overrides if smaller)"/>
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136 </section>
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137 </inputs>
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138
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139 <outputs>
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140 <expand macro="standard_outupt" />
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141 <data format="ps" name="ps_fileA" label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
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142 <filter>'postscript' in outputs</filter>
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143 </data>
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144 <data format="ps" name="ps_fileB" label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
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145 <filter>'postscript' in outputs</filter>
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146 </data>
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147 <data format="txt" name="anchors_fasta" label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
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148 <filter>'anchors-fasta' in outputs</filter>
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149 </data>
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150 <data format="txt" name="anchors_ppA" label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
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151 <filter>'anchors-pp' in outputs</filter>
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152 </data>
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153 <data format="txt" name="anchors_ppB" label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
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154 <filter>'anchors-pp' in outputs</filter>
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155 </data>
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156 <data format="clustal" name="clustal" label="${tool.name} on ${on_string}: chain as alignment (clustal)">
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157 <filter>'clustal' in outputs</filter>
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158 </data>
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159 <data format="tabular" name="epm_list" label="${tool.name} on ${on_string}: list of epms">
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160 <filter>'epm_list' in outputs</filter>
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161 </data>
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162 <data format="tabular" name="chained_epm_list" label="${tool.name} on ${on_string}: list of epms in chain">
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163 <filter>'chained_epm_list' in outputs</filter>
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164 </data>
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165 </outputs>
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166
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167 <tests>
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168 <test expect_num_outputs="2">
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169 <param name="inputA" value="tRNA_2-1.fa"/>
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170 <param name="inputB" value="tRNA_2-2.fa"/>
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171 <param name="outputs" value="epm_list"/>
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172 <output name="epm_list" file="tRNA_2.epms"/>
2
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173 <output name="stdout">
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174 <assert_contents>
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175 <has_text text="LCSEPM preprocessing..."/>
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176 <has_text text="#EPMs:"/>
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177 </assert_contents>
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178 </output>
0
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179 </test>
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180 </tests>
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181
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182 <help><![CDATA[ **LocARNA -- Pairwise matching and folding of RNAs (ExpARNA-P)**
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183
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184 Pairwise matching and folding tool of the LocARNA suite (ExpARNA-P).
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185
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186 **Input.**
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187
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188 Input consists of two sequences or alignments, which are specified in
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189 fasta, clustal, stockholm, or LocARNA pp format.
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190
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191 Optionally, one can specify structure and anchor constraints in these
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192 input files.b
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193
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194 **Output.**
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195
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196 The program enumerates exactly matching local substructures (exact
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197 pattern matches = EPMs) and optionally chains them. It returns lists
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198 of chained and unchained matches, visualizations of the results and
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199 anchor constraints for alignment.
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200
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201
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202 For more information, see
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203 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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204 ]]></help>
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205
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206 <expand macro="citations" />
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207
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208 </tool>