Mercurial > repos > rnateam > mea

annotate mea.xml @ 7:5f780b6d99d3 draft

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author rnateam
date Sat, 01 Aug 2015 04:44:27 -0400
parents 44984b9450ca
children e0f8bc01b84b
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1 <tool id="mea" name="MEA" version="0.6.4.0">
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2 <description>Predict MEA structures and compare structures of RNAs</description>
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3 <requirements>
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4 <requirement type="package" version="2.22.6">gengetopt</requirement>
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5 <requirement type="package" version="0.6.4">mea</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range=":-1"/>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <version_command>mea --version</version_command>
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12 <command><![CDATA[
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13 mea
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14 #if str($predict_mode.predict_selector) == "predict":
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15 $predict_mode.dotplot
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16 #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default"
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17 --alpha $predict_mode.mea_parameters.alpha
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18 --beta $predict_mode.mea_parameters.beta
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19 --gamma $predict_mode.mea_parameters.gamma
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20 --delta $predict_mode.mea_parameters.delta
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21 #end if
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22 #else
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23 --structure `cat $predict_mode.structure`
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24 #end if
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25 #if str($compare_mode.compare_selector) == 'compare':
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26 --reference `cat $compare_mode.reference`
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27 $compare_mode.slide_rule
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28 $compare_mode.conflict_rule
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29 #end if
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30 > $stdout
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31 ]]></command>
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32 <inputs>
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33 <conditional name="predict_mode">
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34 <param name="predict_selector" type="select" label="Predict MEA structure">
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35 <option value="predict">Predict MEA structure</option>
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36 <option value="compare">Specify structure (for comparison)</option>
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37 </param>
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38 <when value="predict">
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39 <param name="dotplot" type="data" format="rna_eps" label="Dotplot" optional="False"
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40 help="Dotplot file (RNA base pair probabilities)"/>
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41 <conditional name="mea_parameters">
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42 <param name="mea_parameters_selector" type="boolean" label="Use default parameters"
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43 truevalue="default" falsevalue="no_default" checked="True"
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44 help="The default parameters assign a base pair weight
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45 of 0.5 and penalize long base pairs." />
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46 <when value="default" />
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47 <when value="no_default">
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48 <param name="alpha" label="Alpha value" type="float"
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49 optional="False" value="0.012"
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50 help="Slope of base pair distance penalty. (--alpha)"/>
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51 <param name="beta" label="Beta value" type="float"
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52 optional="False" value="315"
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53 help="Turning point of base pair distance penalty. (--beta)" />
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54 <param name="gamma" label="Gamma value" type="float"
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55 optional="False" value="0.5"
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56 help="Base pair weight factor. (--gamma)" />
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57 <param name="delta" label="Delta value" type="float"
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58 optional="False" value="0.003"
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59 help="Minimum penalty factor for base pairs. (--delta)" />
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60 </when>
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61 </conditional>
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62 </when>
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63 <when value="compare">
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64 <param name="structure" format="txt" type="data" label="Structure" optional="False"
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65 help="(Predicted) RNA secondary structure for comparison to a reference structure. (--structure)" />
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66 </when>
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67 </conditional>
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68 <conditional name="compare_mode">
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69 <param name="compare_selector" type="select" label="Compare to a reference structure"
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70 help="Whether to compare the predicted (or specified) structure to a reference structure.">
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71 <option value="dont_compare">Do not compare</option>
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72 <option value="compare">Compare to reference structure</option>
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73 </param>
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74 <when value="dont_compare" />
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75 <when value="compare">
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76 <param name="reference"
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77 optional="false"
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78 format="txt" type="data"
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79 label="Reference"
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80 help="Reference structure in dot-bracket format"/>
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81 <param name="slide_rule" label="Slide Rule" type="boolean"
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82 optional="False" checked="True" falsevalue="--no-slide-rule" truevalue="" help="Use slide rule. (--no-slide-rule)" />
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83 <param name="conflict_rule" label="Conflict Rule" type="boolean"
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84 optional="False" checked="True" falsevalue="--no-conflict-rule" truevalue="" help="Use onflict rule. (--no-conflict-rule)"/>
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85 </when>
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86 </conditional>
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87 </inputs>
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88 <outputs>
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89 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="mea_parameter_selector" value="default" />
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94 <param name="predict_selector" value="predict" />
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95 <param name="compare_selector" value="compare" />
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96 <param name="dotplot" value="test_dp.ps" />
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97 <param name="reference" value="test_reference.txt" />
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98 <output name="stdout" file="test_predict.out" />
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99 </test>
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100 <test>
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101 <param name="mea_parameter_selector" value="default" />
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102 <param name="predict_selector" value="compare" />
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103 <param name="compare_selector" value="compare" />
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104 <param name="structure" value="test_structure.txt" />
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105 <param name="reference" value="test_reference.txt" />
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106 <output name="stdout" file="test_compare.out" />
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107 </test>
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108 </tests>
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109 <help><![CDATA[
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110 =====
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111 MEA
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112 =====
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113
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114 `MEA <http://www.bioinf.uni-leipzig.de/Software/mea/>`_ predicts RNA maximum expected accuracy structures from RNA base pair probabilities and optionally compares them to a reference structure. In a special mode it skips the prediction and compares a
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115 given structure to the reference. For the prediction, MEA allows to
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116 penalize long base pairs, using parameters alpha, beta, gamma, and
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117 delta. For the comparison of secondary structures, several measures
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118 are computed from the confusion matrix of the RNA base pairs.
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119
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120 ------
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121 Inputs
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122 ------
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123
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124 The tool accepts dot plot files as generated by RNAfold -p.
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125
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126 For (predicted) structure and reference, the tool accepts
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127 dot-bracket structures with pseudoknots (supporting bracket pairs
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128 (),{},[],<>,Aa,Bb,...)
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129
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130 -------
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131 Outputs
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132 -------
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133
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134 If predicting a structure, the tool outputs the sequence and the
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135 predicted dot bracket strucuture with computed score in parenthesis
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136 following the structure. This mimicks the output of the Vienna
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137 tools.
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138
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139 The result of structure comparison is reported as a line of numbers
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140
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141 TP FP FN TN SENS PPV F1 MCC
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142
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143 where
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144
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145 * TP = # true positives
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146
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147 * FP = # false positives
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148
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149 * FN = # false negatives
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150
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151 * TN = # true negatives
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152
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153 * SENS = TP/(TP+FN) 'Sensitivity'http://www.bioinf.uni-leipzig.de/Software/mea/
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154
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155 * PPV = TP/(TP+FP) 'Positive Predictive Value'
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156
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157 * F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise 'F1-score'
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158
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159 * MCC = (TP*TN - FP*FN) / sqrt( (TP+FP)*(TP+FN)*(TN+FP)*(TN+FN) ) 'Mathews correlation coefficient'
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160
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161
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162 Special rules for prediction evaluation:
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163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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164
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165 * Slide rule: tolerate shift of one base pair end by one base. This
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166 rule directly affects the number of true positives.
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167 * Conflict rule: predicted base pairs are false only if they
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168 conflict with the reference; two base pair conflict if and only if
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169 they share one end This rule directly affects the number of false
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170 positives.
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171
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172 ]]></help>
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173 <citations>
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174 <citation type="doi">10.1007/978-3-319-02624-4_1</citation>
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175 </citations>
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176 </tool>