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annotate mea.xml @ 4:00e0ba24886a draft

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author rnateam
date Wed, 01 Jul 2015 10:50:29 -0400
parents 8c457c7a7bd7
children 12a975bbf94c
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1 <tool id="mea" name="MEA" version="0.6.4.1">
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2 <description>Predict maximum expected accuracy secondary structures
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3 of RNAs and compare RNA secondary structures</description>
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4
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5 <requirements>
1
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6 <requirement type="package" version="2.22.6" >gengetopt</requirement>
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7 <requirement type="package" version="0.6.4" >mea</requirement>
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8 </requirements>
1
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9
0
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10 <stdio>
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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 <command><![CDATA[mea
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15 #if str($mode.mode_selector) == "predict"
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16 $mode.dotplot
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17 --alpha $mode.alpha
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18 --beta $mode.beta
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19 --gamma $mode.gamma
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20 --delta $mode.delta
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21 #else
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22 --structure `cat $mode.structure`
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23 #end if
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24 #if $mode.compare == "compare"
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25 --reference `cat $reference`
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26 $slide_rule
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27 $conflict_rule
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28 #end if
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29 > $stdout
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30 ]]></command>
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31
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32 <inputs>
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33 <conditional name="mode">
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34 <param name="mode_selector" type="select" label="Working Mode">
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35 <option value="predict">Predict</option>
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36 <option value="compare">Compare</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"
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40 optional="false" help="Dotplot file (RNA base pair probabilities)"/>
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41 <param name="alpha" label="Alpha" type="float"
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42 optional="false" value="0.012"
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43 help="Slope of base pair distance penalty"/>
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44 <param name="beta" label="Beta" type="float"
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45 optional="false" value="315"
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46 help="Turning point of base pair distance penalty" />
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47 <param name="gamma" label="Gamma" type="float"
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48 optional="false" value="0.5"
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49 help="Base pair weight factor" />
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50 <param name="delta" label="Delta" type="float"
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51 optional="false" value="0.003"
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52 help="Minimum penalty factor for base pairs" />
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53 </when>
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54 <when value="compare">
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55 <param name="structure" format="txt" type="data" label="Structure"
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56 optional="false" help="(Predicted) RNA secondary structure" />
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57 </when>
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58 </conditional>
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59
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60 <param name="reference" optional="true" format="txt" type="data" label="Reference" />
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61
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62 <param name="slide_rule" label="Slide Rule" type="boolean"
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63 optional="false"
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64 checked="yes"
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65 falsevalue="--no-slide-rule" truevalue=""
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66 help="Use slide rule" />
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67 <param name="conflict_rule" label="Conflict Rule" type="boolean"
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68 optional="false"
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69 checked="yes"
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70 falsevalue="--no-conflict-rule" truevalue=""
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71 help="Use onflict rule"/>
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72 </inputs>
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73
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74 <outputs>
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75 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
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76 </outputs>
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77
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78 <tests>
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79 <test>
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80 <param name="alpha"
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81 value="0.012" />
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82 <param name="beta"
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83 value="315" />
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84 <param name="gamma"
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85 value="0.5" />
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86 <param name="delta"
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87 value="0.003" />
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88 <param name="slide-rule" checked="yes" />
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89 <param name="conflict-rule" checked="yes" />
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90
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91 <param name="mode_selector" value="predict" />
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92 <param name="reference" value="test_reference.txt" />
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93
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94 <param name="dotplot" value="test_dp.ps" />
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95
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96 <output name="stdout" file="test_predict.out" />
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97 </test>
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98
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99 <test>
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100 <param name="mode_selector" value="compare" />
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101 <param name="structure" value="test_structure.txt" />
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102 <param name="reference" value="test_reference.txt" />
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103 <param name="slide-rule" checked="yes" />
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104 <param name="conflict-rule" checked="yes" />
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105
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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
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110
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111 <help><![CDATA[
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112 ===
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113 MEA
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114 ===
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115
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116 MEA predicts RNA maximum expected accuracy structures from RNA base
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117 pair probabilities and optionally compares them to a reference
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118 structure. In a special mode it skips the prediction and compares a
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119 given structure to the reference. For the prediction, MEA allows to
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120 penalize long base pairs, using parameters alpha, beta, gamma, and
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121 delta. For the comparison of secondary structures, several measures
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122 are computed from the confusion matrix of the RNA base pairs.
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123
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124 ------
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125 Inputs
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126 ------
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127
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128 The tool accepts dot plot files as generated by RNAfold -p.
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129
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130 For (predicted) structure and reference, the tool accepts
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131 dot-bracket structures with pseudoknots (supporting bracket pairs
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132 (),{},[],<>,Aa,Bb,...)
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133
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134 -------
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135 Outputs
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136 -------
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137
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138 If predicting a structure, the tool outputs the sequence and the
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139 predicted dot bracket strucuture with computed score in parenthesis
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140 following the structure. This mimicks the output of the Vienna
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141 tools.
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142
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143 The result of structure comparison is reported as a line of numbers
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144
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145 TP FP FN TN SENS PPV F1 MCC
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146
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147 where
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148
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149 * TP = # true positives
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150
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151 * FP = # false positives
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152
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153 * FN = # false negatives
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154
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155 * TN = # true negatives
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156
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157 * SENS = TP/(TP+FN) 'Sensitivity'
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158
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159 * PPV = TP/(TP+FP) 'Positive Predictive Value'
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160
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161 * F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise 'F1-score'
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162
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163 * MCC = (TP*TN - FP*FN) / sqrt( (TP+FP)*(TP+FN)*(TN+FP)*(TN+FN) ) 'Mathews correlation coefficient'
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164
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165
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166 Special rules for prediction evaluation:
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167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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168
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169 * Slide rule: tolerate shift of one base pair end by one base. This
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170 rule directly affects the number of true positives.
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171
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172 * Conflict rule: predicted base pairs are false only if they
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173 conflict with the reference; two base pair conflict if and only if
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174 they share one end This rule directly affects the number of false
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175 positives.
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176
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177 --------
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178 Download
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179 --------
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180
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181 The command line tool MEA is free software available for download and
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182 local installation at
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183 .. __: http://www.bioinf.uni-leipzig.de/Software/mea/
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184
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185 ]]></help>
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186 <citations>
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187 <citation type="doi">10.1007/978-3-319-02624-4_1</citation>
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188 </citations>
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189
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190 </tool>