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planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
author rnateam
date Mon, 06 Jul 2015 05:33:34 -0400
parents 00e0ba24886a
children 44984b9450ca
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4:00e0ba24886a 5:12a975bbf94c
1 <tool id="mea" name="MEA" version="0.6.4.1"> 1 <tool id="mea" name="MEA" version="0.6.4.1">
2 <description>Predict maximum expected accuracy secondary structures 2 <description>Predict MEA structures and compare structures of RNAs</description>
3 of RNAs and compare RNA secondary structures</description> 3
4 4 <requirements>
5 <requirements> 5 <requirement type="package" version="2.22.6" >gengetopt</requirement>
6 <requirement type="package" version="2.22.6" >gengetopt</requirement> 6 <requirement type="package" version="0.6.4" >mea</requirement>
7 <requirement type="package" version="0.6.4" >mea</requirement> 7 </requirements>
8 </requirements> 8
9 9 <stdio>
10 <stdio> 10 <exit_code range=":-1"/>
11 <exit_code range="1:" /> 11 <exit_code range="1:" />
12 </stdio> 12 </stdio>
13 13
14 <command><![CDATA[mea 14 <version_command>mea --version</version_command>
15 #if str($mode.mode_selector) == "predict" 15
16 $mode.dotplot 16 <command><![CDATA[
17 --alpha $mode.alpha 17 mea
18 --beta $mode.beta 18 #if str($predict_mode.predict_selector) == "predict"
19 --gamma $mode.gamma 19 $predict_mode.dotplot
20 --delta $mode.delta 20 #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default"
21 #else 21 --alpha $predict_mode.mea_parameters.alpha
22 --structure `cat $mode.structure` 22 --beta $predict_mode.mea_parameters.beta
23 #end if 23 --gamma $predict_mode.mea_parameters.gamma
24 #if $mode.compare == "compare" 24 --delta $predict_mode.mea_parameters.delta
25 --reference `cat $reference` 25 #end if
26 $slide_rule 26 #else
27 $conflict_rule 27 --structure `cat $predict_mode.structure`
28 #end if 28 #end if
29 > $stdout 29 #if $compare_mode.compare_selector
30 ]]></command> 30 --reference `cat $compare_mode.reference`
31 31 $compare_mode.slide_rule
32 <inputs> 32 $compare_mode.conflict_rule
33 <conditional name="mode"> 33 #end if
34 <param name="mode_selector" type="select" label="Working Mode"> 34 > $stdout
35 <option value="predict">Predict</option> 35 ]]></command>
36 <option value="compare">Compare</option> 36
37 </param> 37 <inputs>
38 <when value="predict"> 38 <conditional name="predict_mode">
39 <param name="dotplot" type="data" format="rna_eps" label="Dotplot" 39 <param name="predict_selector" type="select" label="Predict MEA structure">
40 optional="false" help="Dotplot file (RNA base pair probabilities)"/> 40 <option value="predict">Predict MEA structure</option>
41 <param name="alpha" label="Alpha" type="float" 41 <option value="compare">Specify structure (for comparison)</option>
42 optional="false" value="0.012" 42 </param>
43 help="Slope of base pair distance penalty"/> 43 <when value="predict">
44 <param name="beta" label="Beta" type="float" 44 <param name="dotplot" type="data" format="rna_eps" label="Dotplot"
45 optional="false" value="315" 45 optional="false" help="Dotplot file (RNA base pair probabilities)"/>
46 help="Turning point of base pair distance penalty" /> 46 <conditional name="mea_parameters">
47 <param name="gamma" label="Gamma" type="float" 47 <param name="mea_parameters_selector"
48 optional="false" value="0.5" 48 type="boolean"
49 help="Base pair weight factor" /> 49 label="Use default parameters"
50 <param name="delta" label="Delta" type="float" 50 truevalue="default"
51 optional="false" value="0.003" 51 falsevalue="no_default"
52 help="Minimum penalty factor for base pairs" /> 52 checked="yes"
53 </when> 53 help="The default parameters assign a base pair weight
54 <when value="compare"> 54 of 0.5 and penalize long base pairs."
55 <param name="structure" format="txt" type="data" label="Structure" 55 />
56 optional="false" help="(Predicted) RNA secondary structure" /> 56 <when value="default" />
57 </when> 57 <when value="no_default">
58 </conditional> 58 <param name="alpha" label="Alpha" type="float"
59 59 optional="false" value="0.012"
60 <param name="reference" optional="true" format="txt" type="data" label="Reference" /> 60 help="Slope of base pair distance penalty"/>
61 61 <param name="beta" label="Beta" type="float"
62 <param name="slide_rule" label="Slide Rule" type="boolean" 62 optional="false" value="315"
63 optional="false" 63 help="Turning point of base pair distance penalty" />
64 checked="yes" 64 <param name="gamma" label="Gamma" type="float"
65 falsevalue="--no-slide-rule" truevalue="" 65 optional="false" value="0.5"
66 help="Use slide rule" /> 66 help="Base pair weight factor" />
67 <param name="conflict_rule" label="Conflict Rule" type="boolean" 67 <param name="delta" label="Delta" type="float"
68 optional="false" 68 optional="false" value="0.003"
69 checked="yes" 69 help="Minimum penalty factor for base pairs" />
70 falsevalue="--no-conflict-rule" truevalue="" 70 </when>
71 help="Use onflict rule"/> 71 </conditional>
72 </inputs> 72 </when>
73 73 <when value="compare">
74 <outputs> 74 <param name="structure" format="txt" type="data" label="Structure"
75 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" /> 75 optional="false"
76 </outputs> 76 help="(Predicted) RNA secondary structure
77 77 for comparison to a reference structure." />
78 <tests> 78 </when>
79 <test> 79 </conditional>
80 <param name="alpha" 80
81 value="0.012" /> 81
82 <param name="beta" 82 <conditional name="compare_mode">
83 value="315" /> 83 <param name="compare_selector"
84 <param name="gamma" 84 type="boolean"
85 value="0.5" /> 85 label="Compare to a reference structure"
86 <param name="delta" 86 optional="false"
87 value="0.003" /> 87 checked="false"
88 <param name="slide-rule" checked="yes" /> 88 truevalue="compare"
89 <param name="conflict-rule" checked="yes" /> 89 falsevalue="dont_compare"
90 90 help="Whether to compare the predicted (or specified) structure
91 <param name="mode_selector" value="predict" /> 91 to a reference structure."
92 <param name="reference" value="test_reference.txt" /> 92 />
93 93 <when value="dont_compare" />
94 <param name="dotplot" value="test_dp.ps" /> 94 <when value="compare">
95 95 <param name="reference"
96 <output name="stdout" file="test_predict.out" /> 96 optional="true"
97 </test> 97 format="txt" type="data"
98 98 label="Reference"
99 <test> 99 help="Reference structure in dot-bracket format"/>
100 <param name="mode_selector" value="compare" /> 100
101 <param name="structure" value="test_structure.txt" /> 101 <param name="slide_rule" label="Slide Rule" type="boolean"
102 <param name="reference" value="test_reference.txt" /> 102 optional="false"
103 <param name="slide-rule" checked="yes" /> 103 checked="yes"
104 <param name="conflict-rule" checked="yes" /> 104 falsevalue="--no-slide-rule" truevalue=""
105 105 help="Use slide rule" />
106 <output name="stdout" file="test_compare.out" /> 106 <param name="conflict_rule" label="Conflict Rule" type="boolean"
107 </test> 107 optional="false"
108 </tests> 108 checked="yes"
109 109 falsevalue="--no-conflict-rule" truevalue=""
110 110 help="Use onflict rule"/>
111 <help><![CDATA[ 111 </when>
112 === 112 </conditional>
113 </inputs>
114
115 <outputs>
116 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
117 </outputs>
118
119 <tests>
120 <test>
121 <param name="mea_parameter_selector" value="default" />
122
123 <param name="predict_selector" value="predict" />
124 <param name="compare_selector" value="true" />
125
126 <param name="dotplot" value="test_dp.ps" />
127 <param name="reference" value="test_reference.txt" />
128
129 <output name="stdout" file="test_predict.out" />
130 </test>
131
132 <test>
133 <param name="mea_parameter_selector" value="default" />
134 <param name="predict_selector" value="compare" />
135 <param name="compare_selector" value="true" />
136
137 <param name="structure" value="test_structure.txt" />
138 <param name="reference" value="test_reference.txt" />
139
140 <output name="stdout" file="test_compare.out" />
141 </test>
142 </tests>
143
144
145 <help><![CDATA[
146 =====
113 MEA 147 MEA
114 === 148 =====
115 149
116 MEA predicts RNA maximum expected accuracy structures from RNA base 150 MEA predicts RNA maximum expected accuracy structures from RNA base
117 pair probabilities and optionally compares them to a reference 151 pair probabilities and optionally compares them to a reference
118 structure. In a special mode it skips the prediction and compares a 152 structure. In a special mode it skips the prediction and compares a
119 given structure to the reference. For the prediction, MEA allows to 153 given structure to the reference. For the prediction, MEA allows to
120 penalize long base pairs, using parameters alpha, beta, gamma, and 154 penalize long base pairs, using parameters alpha, beta, gamma, and
122 are computed from the confusion matrix of the RNA base pairs. 156 are computed from the confusion matrix of the RNA base pairs.
123 157
124 ------ 158 ------
125 Inputs 159 Inputs
126 ------ 160 ------
127 161
128 The tool accepts dot plot files as generated by RNAfold -p. 162 The tool accepts dot plot files as generated by RNAfold -p.
129 163
130 For (predicted) structure and reference, the tool accepts 164 For (predicted) structure and reference, the tool accepts
131 dot-bracket structures with pseudoknots (supporting bracket pairs 165 dot-bracket structures with pseudoknots (supporting bracket pairs
132 (),{},[],<>,Aa,Bb,...) 166 (),{},[],<>,Aa,Bb,...)
133 167
134 ------- 168 -------
135 Outputs 169 Outputs
136 ------- 170 -------
137 171
138 If predicting a structure, the tool outputs the sequence and the 172 If predicting a structure, the tool outputs the sequence and the
139 predicted dot bracket strucuture with computed score in parenthesis 173 predicted dot bracket strucuture with computed score in parenthesis
140 following the structure. This mimicks the output of the Vienna 174 following the structure. This mimicks the output of the Vienna
141 tools. 175 tools.
142 176
143 The result of structure comparison is reported as a line of numbers 177 The result of structure comparison is reported as a line of numbers
144 178
145 TP FP FN TN SENS PPV F1 MCC 179 TP FP FN TN SENS PPV F1 MCC
146 180
147 where 181 where
148 182
149 * TP = # true positives 183 * TP = # true positives
150 184
151 * FP = # false positives 185 * FP = # false positives
152 186
153 * FN = # false negatives 187 * FN = # false negatives
154 188
155 * TN = # true negatives 189 * TN = # true negatives
156 190
157 * SENS = TP/(TP+FN) 'Sensitivity' 191 * SENS = TP/(TP+FN) 'Sensitivity'
158 192
159 * PPV = TP/(TP+FP) 'Positive Predictive Value' 193 * PPV = TP/(TP+FP) 'Positive Predictive Value'
160 194
161 * F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise 'F1-score' 195 * F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise 'F1-score'
162 196
163 * MCC = (TP*TN - FP*FN) / sqrt( (TP+FP)*(TP+FN)*(TN+FP)*(TN+FN) ) 'Mathews correlation coefficient' 197 * MCC = (TP*TN - FP*FN) / sqrt( (TP+FP)*(TP+FN)*(TN+FP)*(TN+FN) ) 'Mathews correlation coefficient'
164 198
165 199
166 Special rules for prediction evaluation: 200 Special rules for prediction evaluation:
167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
168 202
169 * Slide rule: tolerate shift of one base pair end by one base. This 203 * Slide rule: tolerate shift of one base pair end by one base. This
170 rule directly affects the number of true positives. 204 rule directly affects the number of true positives.
171 205
172 * Conflict rule: predicted base pairs are false only if they 206 * Conflict rule: predicted base pairs are false only if they
173 conflict with the reference; two base pair conflict if and only if 207 conflict with the reference; two base pair conflict if and only if
174 they share one end This rule directly affects the number of false 208 they share one end This rule directly affects the number of false
175 positives. 209 positives.
176 210
177 -------- 211 --------
178 Download 212 Download
179 -------- 213 --------
180 214
181 The command line tool MEA is free software available for download and 215 The command line tool MEA is free software available for download and
182 local installation at 216 local installation at
183 .. __: http://www.bioinf.uni-leipzig.de/Software/mea/ 217 .. __: http://www.bioinf.uni-leipzig.de/Software/mea/
184 218 ]]></help>
185 ]]></help> 219 <citations>
186 <citations> 220 <citation type="doi">10.1007/978-3-319-02624-4_1</citation>
187 <citation type="doi">10.1007/978-3-319-02624-4_1</citation> 221 </citations>
188 </citations>
189 222
190 </tool> 223 </tool>