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annotate mea.xml @ 8:e0f8bc01b84b draft

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author rnateam
date Thu, 10 Dec 2015 12:22:08 -0500
parents 5f780b6d99d3
children ee79a49755da
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1 <tool id="mea" name="MEA" version="0.6.4.1">
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2 <description>Predict MEA structures and compare structures of RNAs</description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.22.6" >gengetopt</requirement>
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6 <requirement type="package" version="0.6.4" >mea</requirement>
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7 </requirements>
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8
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9 <stdio>
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10 <exit_code range=":-1"/>
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11 <exit_code range="1:" />
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12 </stdio>
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13
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14 <version_command>mea --version</version_command>
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15
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16 <command><![CDATA[
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17 mea
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18 #if str($predict_mode.predict_selector) == "predict"
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19 $predict_mode.dotplot
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20 #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default"
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21 --alpha $predict_mode.mea_parameters.alpha
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22 --beta $predict_mode.mea_parameters.beta
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23 --gamma $predict_mode.mea_parameters.gamma
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24 --delta $predict_mode.mea_parameters.delta
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25 #end if
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26 #else
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27 --structure `cat $predict_mode.structure`
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28 #end if
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29 #if $compare_mode.compare_selector
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30 --reference `cat $compare_mode.reference`
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31 $compare_mode.slide_rule
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32 $compare_mode.conflict_rule
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33 #end if
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34 > $stdout
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35 ]]></command>
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36
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37 <inputs>
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38 <conditional name="predict_mode">
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39 <param name="predict_selector" type="select" label="Predict MEA structure">
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40 <option value="predict">Predict MEA structure</option>
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41 <option value="compare">Specify structure (for comparison)</option>
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42 </param>
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43 <when value="predict">
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44 <param name="dotplot" type="data" format="rna_eps" label="Dotplot"
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45 optional="false" help="Dotplot file (RNA base pair probabilities)"/>
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46 <conditional name="mea_parameters">
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47 <param name="mea_parameters_selector"
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48 type="boolean"
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49 label="Use default parameters"
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50 truevalue="default"
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51 falsevalue="no_default"
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52 checked="yes"
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53 help="The default parameters assign a base pair weight
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54 of 0.5 and penalize long base pairs."
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55 />
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56 <when value="default" />
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57 <when value="no_default">
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58 <param name="alpha" label="Alpha" type="float"
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59 optional="false" value="0.012"
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60 help="Slope of base pair distance penalty"/>
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61 <param name="beta" label="Beta" type="float"
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62 optional="false" value="315"
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63 help="Turning point of base pair distance penalty" />
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64 <param name="gamma" label="Gamma" type="float"
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65 optional="false" value="0.5"
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66 help="Base pair weight factor" />
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67 <param name="delta" label="Delta" type="float"
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68 optional="false" value="0.003"
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69 help="Minimum penalty factor for base pairs" />
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70 </when>
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71 </conditional>
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72 </when>
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73 <when value="compare">
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74 <param name="structure" format="txt" type="data" label="Structure"
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75 optional="false"
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76 help="(Predicted) RNA secondary structure
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77 for comparison to a reference structure." />
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78 </when>
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79 </conditional>
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80
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81
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82 <conditional name="compare_mode">
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83 <param name="compare_selector"
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84 type="boolean"
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85 label="Compare to a reference structure"
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86 optional="false"
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87 checked="false"
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88 truevalue="compare"
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89 falsevalue="dont_compare"
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90 help="Whether to compare the predicted (or specified) structure
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91 to a reference structure."
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92 />
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93 <when value="dont_compare" />
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94 <when value="compare">
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95 <param name="reference"
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96 optional="false"
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97 format="txt" type="data"
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98 label="Reference"
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99 help="Reference structure in dot-bracket format"/>
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100
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101 <param name="slide_rule" label="Slide Rule" type="boolean"
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102 optional="false"
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103 checked="yes"
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104 falsevalue="--no-slide-rule" truevalue=""
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105 help="Use slide rule" />
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106 <param name="conflict_rule" label="Conflict Rule" type="boolean"
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107 optional="false"
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108 checked="yes"
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109 falsevalue="--no-conflict-rule" truevalue=""
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110 help="Use onflict rule"/>
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111 </when>
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112 </conditional>
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113 </inputs>
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114
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115 <outputs>
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116 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
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117 </outputs>
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118
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119 <tests>
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120 <test>
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121 <param name="mea_parameter_selector" value="default" />
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122
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123 <param name="predict_selector" value="predict" />
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124 <param name="compare_selector" value="true" />
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125
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126 <param name="dotplot" value="test_dp.ps" />
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127 <param name="reference" value="test_reference.txt" />
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128
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129 <output name="stdout" file="test_predict.out" />
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130 </test>
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131
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132 <test>
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133 <param name="mea_parameter_selector" value="default" />
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134 <param name="predict_selector" value="compare" />
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135 <param name="compare_selector" value="true" />
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136
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137 <param name="structure" value="test_structure.txt" />
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138 <param name="reference" value="test_reference.txt" />
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139
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140 <output name="stdout" file="test_compare.out" />
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141 </test>
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142 </tests>
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143
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144
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145 <help><![CDATA[
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146 =====
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147 MEA
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148 =====
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149
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150 MEA predicts RNA maximum expected accuracy structures from RNA base
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151 pair probabilities and optionally compares them to a reference
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152 structure. In a special mode it skips the prediction and compares a
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153 given structure to the reference. For the prediction, MEA allows to
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154 penalize long base pairs, using parameters alpha, beta, gamma, and
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155 delta. For the comparison of secondary structures, several measures
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156 are computed from the confusion matrix of the RNA base pairs.
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157
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158 ------
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159 Inputs
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160 ------
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161
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162 The tool accepts dot plot files as generated by RNAfold -p.
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163
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164 For (predicted) structure and reference, the tool accepts
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165 dot-bracket structures with pseudoknots (supporting bracket pairs
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166 (),{},[],<>,Aa,Bb,...)
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167
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168 -------
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169 Outputs
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170 -------
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171
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172 If predicting a structure, the tool outputs the sequence and the
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173 predicted dot bracket strucuture with computed score in parenthesis
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174 following the structure. This mimicks the output of the Vienna
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175 tools.
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176
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177 The result of structure comparison is reported as a line of numbers
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178
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179 TP FP FN TN SENS PPV F1 MCC
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180
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181 where
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182
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183 * TP = # true positives
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184
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185 * FP = # false positives
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186
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187 * FN = # false negatives
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188
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189 * TN = # true negatives
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190
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191 * SENS = TP/(TP+FN) 'Sensitivity'
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192
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193 * PPV = TP/(TP+FP) 'Positive Predictive Value'
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194
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195 * F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise 'F1-score'
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196
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197 * MCC = (TP*TN - FP*FN) / sqrt( (TP+FP)*(TP+FN)*(TN+FP)*(TN+FN) ) 'Mathews correlation coefficient'
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198
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199
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200 Special rules for prediction evaluation:
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201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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202
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203 * Slide rule: tolerate shift of one base pair end by one base. This
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204 rule directly affects the number of true positives.
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205
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206 * Conflict rule: predicted base pairs are false only if they
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207 conflict with the reference; two base pair conflict if and only if
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208 they share one end This rule directly affects the number of false
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209 positives.
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210
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211 --------
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212 Download
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213 --------
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214
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215 The command line tool MEA is free software available for download and
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216 local installation at
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217 .. __: http://www.bioinf.uni-leipzig.de/Software/mea/
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218 ]]></help>
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219 <citations>
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220 <citation type="doi">10.1007/978-3-319-02624-4_1</citation>
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221 </citations>
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222
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223 </tool>