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planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
author rnateam
date Thu, 10 Dec 2015 12:22:08 -0500
parents 5f780b6d99d3
children ee79a49755da
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7:5f780b6d99d3 8:e0f8bc01b84b
1 <tool id="mea" name="MEA" version="0.6.4.0"> 1 <tool id="mea" name="MEA" version="0.6.4.1">
2 <description>Predict MEA structures and compare structures of RNAs</description> 2 <description>Predict MEA structures and compare structures of RNAs</description>
3
3 <requirements> 4 <requirements>
4 <requirement type="package" version="2.22.6">gengetopt</requirement> 5 <requirement type="package" version="2.22.6" >gengetopt</requirement>
5 <requirement type="package" version="0.6.4">mea</requirement> 6 <requirement type="package" version="0.6.4" >mea</requirement>
6 </requirements> 7 </requirements>
8
7 <stdio> 9 <stdio>
8 <exit_code range=":-1"/> 10 <exit_code range=":-1"/>
9 <exit_code range="1:" /> 11 <exit_code range="1:" />
10 </stdio> 12 </stdio>
13
11 <version_command>mea --version</version_command> 14 <version_command>mea --version</version_command>
15
12 <command><![CDATA[ 16 <command><![CDATA[
13 mea 17 mea
14 #if str($predict_mode.predict_selector) == "predict": 18 #if str($predict_mode.predict_selector) == "predict"
15 $predict_mode.dotplot 19 $predict_mode.dotplot
16 #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default" 20 #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default"
17 --alpha $predict_mode.mea_parameters.alpha 21 --alpha $predict_mode.mea_parameters.alpha
18 --beta $predict_mode.mea_parameters.beta 22 --beta $predict_mode.mea_parameters.beta
19 --gamma $predict_mode.mea_parameters.gamma 23 --gamma $predict_mode.mea_parameters.gamma
20 --delta $predict_mode.mea_parameters.delta 24 --delta $predict_mode.mea_parameters.delta
21 #end if 25 #end if
22 #else 26 #else
23 --structure `cat $predict_mode.structure` 27 --structure `cat $predict_mode.structure`
24 #end if 28 #end if
25 #if str($compare_mode.compare_selector) == 'compare': 29 #if $compare_mode.compare_selector
26 --reference `cat $compare_mode.reference` 30 --reference `cat $compare_mode.reference`
27 $compare_mode.slide_rule 31 $compare_mode.slide_rule
28 $compare_mode.conflict_rule 32 $compare_mode.conflict_rule
29 #end if 33 #end if
30 > $stdout 34 > $stdout
31 ]]></command> 35 ]]></command>
36
32 <inputs> 37 <inputs>
33 <conditional name="predict_mode"> 38 <conditional name="predict_mode">
34 <param name="predict_selector" type="select" label="Predict MEA structure"> 39 <param name="predict_selector" type="select" label="Predict MEA structure">
35 <option value="predict">Predict MEA structure</option> 40 <option value="predict">Predict MEA structure</option>
36 <option value="compare">Specify structure (for comparison)</option> 41 <option value="compare">Specify structure (for comparison)</option>
37 </param> 42 </param>
38 <when value="predict"> 43 <when value="predict">
39 <param name="dotplot" type="data" format="rna_eps" label="Dotplot" optional="False" 44 <param name="dotplot" type="data" format="rna_eps" label="Dotplot"
40 help="Dotplot file (RNA base pair probabilities)"/> 45 optional="false" help="Dotplot file (RNA base pair probabilities)"/>
41 <conditional name="mea_parameters"> 46 <conditional name="mea_parameters">
42 <param name="mea_parameters_selector" type="boolean" label="Use default parameters" 47 <param name="mea_parameters_selector"
43 truevalue="default" falsevalue="no_default" checked="True" 48 type="boolean"
44 help="The default parameters assign a base pair weight 49 label="Use default parameters"
45 of 0.5 and penalize long base pairs." /> 50 truevalue="default"
46 <when value="default" /> 51 falsevalue="no_default"
47 <when value="no_default"> 52 checked="yes"
48 <param name="alpha" label="Alpha value" type="float" 53 help="The default parameters assign a base pair weight
49 optional="False" value="0.012" 54 of 0.5 and penalize long base pairs."
50 help="Slope of base pair distance penalty. (--alpha)"/> 55 />
51 <param name="beta" label="Beta value" type="float" 56 <when value="default" />
52 optional="False" value="315" 57 <when value="no_default">
53 help="Turning point of base pair distance penalty. (--beta)" /> 58 <param name="alpha" label="Alpha" type="float"
54 <param name="gamma" label="Gamma value" type="float" 59 optional="false" value="0.012"
55 optional="False" value="0.5" 60 help="Slope of base pair distance penalty"/>
56 help="Base pair weight factor. (--gamma)" /> 61 <param name="beta" label="Beta" type="float"
57 <param name="delta" label="Delta value" type="float" 62 optional="false" value="315"
58 optional="False" value="0.003" 63 help="Turning point of base pair distance penalty" />
59 help="Minimum penalty factor for base pairs. (--delta)" /> 64 <param name="gamma" label="Gamma" type="float"
60 </when> 65 optional="false" value="0.5"
61 </conditional> 66 help="Base pair weight factor" />
62 </when> 67 <param name="delta" label="Delta" type="float"
63 <when value="compare"> 68 optional="false" value="0.003"
64 <param name="structure" format="txt" type="data" label="Structure" optional="False" 69 help="Minimum penalty factor for base pairs" />
65 help="(Predicted) RNA secondary structure for comparison to a reference structure. (--structure)" /> 70 </when>
66 </when> 71 </conditional>
67 </conditional> 72 </when>
68 <conditional name="compare_mode"> 73 <when value="compare">
69 <param name="compare_selector" type="select" label="Compare to a reference structure" 74 <param name="structure" format="txt" type="data" label="Structure"
70 help="Whether to compare the predicted (or specified) structure to a reference structure."> 75 optional="false"
71 <option value="dont_compare">Do not compare</option> 76 help="(Predicted) RNA secondary structure
72 <option value="compare">Compare to reference structure</option> 77 for comparison to a reference structure." />
73 </param> 78 </when>
74 <when value="dont_compare" /> 79 </conditional>
75 <when value="compare"> 80
76 <param name="reference" 81
77 optional="false" 82 <conditional name="compare_mode">
78 format="txt" type="data" 83 <param name="compare_selector"
79 label="Reference" 84 type="boolean"
80 help="Reference structure in dot-bracket format"/> 85 label="Compare to a reference structure"
81 <param name="slide_rule" label="Slide Rule" type="boolean" 86 optional="false"
82 optional="False" checked="True" falsevalue="--no-slide-rule" truevalue="" help="Use slide rule. (--no-slide-rule)" /> 87 checked="false"
83 <param name="conflict_rule" label="Conflict Rule" type="boolean" 88 truevalue="compare"
84 optional="False" checked="True" falsevalue="--no-conflict-rule" truevalue="" help="Use onflict rule. (--no-conflict-rule)"/> 89 falsevalue="dont_compare"
85 </when> 90 help="Whether to compare the predicted (or specified) structure
86 </conditional> 91 to a reference structure."
92 />
93 <when value="dont_compare" />
94 <when value="compare">
95 <param name="reference"
96 optional="false"
97 format="txt" type="data"
98 label="Reference"
99 help="Reference structure in dot-bracket format"/>
100
101 <param name="slide_rule" label="Slide Rule" type="boolean"
102 optional="false"
103 checked="yes"
104 falsevalue="--no-slide-rule" truevalue=""
105 help="Use slide rule" />
106 <param name="conflict_rule" label="Conflict Rule" type="boolean"
107 optional="false"
108 checked="yes"
109 falsevalue="--no-conflict-rule" truevalue=""
110 help="Use onflict rule"/>
111 </when>
112 </conditional>
87 </inputs> 113 </inputs>
114
88 <outputs> 115 <outputs>
89 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" /> 116 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
90 </outputs> 117 </outputs>
118
91 <tests> 119 <tests>
92 <test> 120 <test>
93 <param name="mea_parameter_selector" value="default" /> 121 <param name="mea_parameter_selector" value="default" />
94 <param name="predict_selector" value="predict" /> 122
95 <param name="compare_selector" value="compare" /> 123 <param name="predict_selector" value="predict" />
96 <param name="dotplot" value="test_dp.ps" /> 124 <param name="compare_selector" value="true" />
97 <param name="reference" value="test_reference.txt" /> 125
98 <output name="stdout" file="test_predict.out" /> 126 <param name="dotplot" value="test_dp.ps" />
99 </test> 127 <param name="reference" value="test_reference.txt" />
100 <test> 128
101 <param name="mea_parameter_selector" value="default" /> 129 <output name="stdout" file="test_predict.out" />
102 <param name="predict_selector" value="compare" /> 130 </test>
103 <param name="compare_selector" value="compare" /> 131
104 <param name="structure" value="test_structure.txt" /> 132 <test>
105 <param name="reference" value="test_reference.txt" /> 133 <param name="mea_parameter_selector" value="default" />
106 <output name="stdout" file="test_compare.out" /> 134 <param name="predict_selector" value="compare" />
107 </test> 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>
108 </tests> 142 </tests>
143
144
109 <help><![CDATA[ 145 <help><![CDATA[
110 ===== 146 =====
111 MEA 147 MEA
112 ===== 148 =====
113 149
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 150 MEA predicts RNA maximum expected accuracy structures from RNA base
151 pair probabilities and optionally compares them to a reference
152 structure. In a special mode it skips the prediction and compares a
115 given structure to the reference. For the prediction, MEA allows to 153 given structure to the reference. For the prediction, MEA allows to
116 penalize long base pairs, using parameters alpha, beta, gamma, and 154 penalize long base pairs, using parameters alpha, beta, gamma, and
117 delta. For the comparison of secondary structures, several measures 155 delta. For the comparison of secondary structures, several measures
118 are computed from the confusion matrix of the RNA base pairs. 156 are computed from the confusion matrix of the RNA base pairs.
119 157
148 186
149 * FN = # false negatives 187 * FN = # false negatives
150 188
151 * TN = # true negatives 189 * TN = # true negatives
152 190
153 * SENS = TP/(TP+FN) 'Sensitivity'http://www.bioinf.uni-leipzig.de/Software/mea/ 191 * SENS = TP/(TP+FN) 'Sensitivity'
154 192
155 * PPV = TP/(TP+FP) 'Positive Predictive Value' 193 * PPV = TP/(TP+FP) 'Positive Predictive Value'
156 194
157 * 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'
158 196
161 199
162 Special rules for prediction evaluation: 200 Special rules for prediction evaluation:
163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
164 202
165 * 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
166 rule directly affects the number of true positives. 204 rule directly affects the number of true positives.
205
167 * Conflict rule: predicted base pairs are false only if they 206 * Conflict rule: predicted base pairs are false only if they
168 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
169 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
170 positives. 209 positives.
171 210
211 --------
212 Download
213 --------
214
215 The command line tool MEA is free software available for download and
216 local installation at
217 .. __: http://www.bioinf.uni-leipzig.de/Software/mea/
172 ]]></help> 218 ]]></help>
173 <citations> 219 <citations>
174 <citation type="doi">10.1007/978-3-319-02624-4_1</citation> 220 <citation type="doi">10.1007/978-3-319-02624-4_1</citation>
175 </citations> 221 </citations>
222
176 </tool> 223 </tool>