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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea commit 6767a5ffb02052c844e9d862c79912f998f39d8e
author rnateam
date Mon, 20 Nov 2017 05:03:35 -0500
parents e0f8bc01b84b
children
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8:e0f8bc01b84b 9:ee79a49755da
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 MEA structures and compare structures of RNAs</description> 2 <description>Predict MEA structures and compare structures of RNAs</description>
3
4 <requirements> 3 <requirements>
5 <requirement type="package" version="2.22.6" >gengetopt</requirement> 4 <requirement type="package" version="0.6.4">mea</requirement>
6 <requirement type="package" version="0.6.4" >mea</requirement>
7 </requirements> 5 </requirements>
8
9 <stdio>
10 <exit_code range=":-1"/>
11 <exit_code range="1:" />
12 </stdio>
13
14 <version_command>mea --version</version_command> 6 <version_command>mea --version</version_command>
15 7 <command detect_errors="aggressive"><![CDATA[
16 <command><![CDATA[
17 mea 8 mea
18 #if str($predict_mode.predict_selector) == "predict" 9 #if str($predict_mode.predict_selector) == 'predict':
19 $predict_mode.dotplot 10 '$predict_mode.dotplot'
20 #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default" 11 #if str($predict_mode.mea_parameters.mea_parameters_selector) == 'no_default'
21 --alpha $predict_mode.mea_parameters.alpha 12 --alpha $predict_mode.mea_parameters.alpha
22 --beta $predict_mode.mea_parameters.beta 13 --beta $predict_mode.mea_parameters.beta
23 --gamma $predict_mode.mea_parameters.gamma 14 --gamma $predict_mode.mea_parameters.gamma
24 --delta $predict_mode.mea_parameters.delta 15 --delta $predict_mode.mea_parameters.delta
25 #end if 16 #end if
26 #else 17 #else
27 --structure `cat $predict_mode.structure` 18 --structure '$predict_mode.structure'
28 #end if 19 #end if
29 #if $compare_mode.compare_selector 20 #if str($compare_mode.compare_selector) == 'compare':
30 --reference `cat $compare_mode.reference` 21 --reference '$compare_mode.reference'
31 $compare_mode.slide_rule 22 $compare_mode.slide_rule
32 $compare_mode.conflict_rule 23 $compare_mode.conflict_rule
33 #end if 24 #end if
34 > $stdout 25 > $stdout
35 ]]></command> 26 ]]></command>
36
37 <inputs> 27 <inputs>
38 <conditional name="predict_mode"> 28 <conditional name="predict_mode">
39 <param name="predict_selector" type="select" label="Predict MEA structure"> 29 <param name="predict_selector" type="select" label="Predict MEA structure">
40 <option value="predict">Predict MEA structure</option> 30 <option value="predict">Predict MEA structure</option>
41 <option value="compare">Specify structure (for comparison)</option> 31 <option value="compare">Specify structure (for comparison)</option>
42 </param> 32 </param>
43 <when value="predict"> 33 <when value="predict">
44 <param name="dotplot" type="data" format="rna_eps" label="Dotplot" 34 <param name="dotplot" type="data" format="rna_eps" label="Dotplot" optional="False"
45 optional="false" help="Dotplot file (RNA base pair probabilities)"/> 35 help="Dotplot file (RNA base pair probabilities)"/>
46 <conditional name="mea_parameters"> 36 <conditional name="mea_parameters">
47 <param name="mea_parameters_selector" 37 <param name="mea_parameters_selector" type="boolean" label="Use default parameters"
48 type="boolean" 38 truevalue="default" falsevalue="no_default" checked="True"
49 label="Use default parameters" 39 help="The default parameters assign a base pair weight
50 truevalue="default" 40 of 0.5 and penalize long base pairs." />
51 falsevalue="no_default" 41 <when value="default" />
52 checked="yes" 42 <when value="no_default">
53 help="The default parameters assign a base pair weight 43 <param name="alpha" label="Alpha value" type="float"
54 of 0.5 and penalize long base pairs." 44 optional="False" value="0.012"
55 /> 45 help="Slope of base pair distance penalty. (--alpha)"/>
56 <when value="default" /> 46 <param name="beta" label="Beta value" type="float"
57 <when value="no_default"> 47 optional="False" value="315"
58 <param name="alpha" label="Alpha" type="float" 48 help="Turning point of base pair distance penalty. (--beta)" />
59 optional="false" value="0.012" 49 <param name="gamma" label="Gamma value" type="float"
60 help="Slope of base pair distance penalty"/> 50 optional="False" value="0.5"
61 <param name="beta" label="Beta" type="float" 51 help="Base pair weight factor. (--gamma)" />
62 optional="false" value="315" 52 <param name="delta" label="Delta value" type="float"
63 help="Turning point of base pair distance penalty" /> 53 optional="False" value="0.003"
64 <param name="gamma" label="Gamma" type="float" 54 help="Minimum penalty factor for base pairs. (--delta)" />
65 optional="false" value="0.5" 55 </when>
66 help="Base pair weight factor" /> 56 </conditional>
67 <param name="delta" label="Delta" type="float" 57 </when>
68 optional="false" value="0.003" 58 <when value="compare">
69 help="Minimum penalty factor for base pairs" /> 59 <param argument="--structure" type="text" label="Structure" optional="False"
70 </when> 60 help="(Predicted) RNA secondary structure for comparison to a reference structure in dot-bracket format">
71 </conditional> 61 <sanitizer>
72 </when> 62 <valid>
73 <when value="compare"> 63 <add value="("/>
74 <param name="structure" format="txt" type="data" label="Structure" 64 <add value=")"/>
75 optional="false" 65 <add value="."/>
76 help="(Predicted) RNA secondary structure 66 </valid>
77 for comparison to a reference structure." /> 67 </sanitizer>
78 </when> 68 </param>
79 </conditional> 69 </when>
80 70 </conditional>
81 71 <conditional name="compare_mode">
82 <conditional name="compare_mode"> 72 <param name="compare_selector" type="select" label="Compare to a reference structure"
83 <param name="compare_selector" 73 help="Whether to compare the predicted (or specified) structure to a reference structure.">
84 type="boolean" 74 <option value="dont_compare">Do not compare</option>
85 label="Compare to a reference structure" 75 <option value="compare">Compare to reference structure</option>
86 optional="false" 76 </param>
87 checked="false" 77 <when value="dont_compare" />
88 truevalue="compare" 78 <when value="compare">
89 falsevalue="dont_compare" 79 <param name="reference" optional="false" type="text" label="Reference"
90 help="Whether to compare the predicted (or specified) structure 80 help="Reference structure in dot-bracket format">
91 to a reference structure." 81 <sanitizer>
92 /> 82 <valid>
93 <when value="dont_compare" /> 83 <add value="("/>
94 <when value="compare"> 84 <add value=")"/>
95 <param name="reference" 85 <add value="."/>
96 optional="false" 86 </valid>
97 format="txt" type="data" 87 </sanitizer>
98 label="Reference" 88 </param>
99 help="Reference structure in dot-bracket format"/> 89 <param name="slide_rule" label="Slide Rule" type="boolean"
100 90 optional="False" checked="True" falsevalue="--no-slide-rule" truevalue="" help="Use slide rule. (--no-slide-rule)" />
101 <param name="slide_rule" label="Slide Rule" type="boolean" 91 <param name="conflict_rule" label="Conflict Rule" type="boolean"
102 optional="false" 92 optional="False" checked="True" falsevalue="--no-conflict-rule" truevalue="" help="Use onflict rule. (--no-conflict-rule)"/>
103 checked="yes" 93 </when>
104 falsevalue="--no-slide-rule" truevalue="" 94 </conditional>
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>
113 </inputs> 95 </inputs>
114
115 <outputs> 96 <outputs>
116 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" /> 97 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
117 </outputs> 98 </outputs>
118
119 <tests> 99 <tests>
120 <test> 100 <test>
121 <param name="mea_parameter_selector" value="default" /> 101 <param name="mea_parameter_selector" value="default" />
122 102 <param name="predict_selector" value="predict" />
123 <param name="predict_selector" value="predict" /> 103 <param name="compare_selector" value="compare" />
124 <param name="compare_selector" value="true" /> 104 <param name="dotplot" value="test_dp.ps" />
125 105 <param name="reference" value=".....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))" />
126 <param name="dotplot" value="test_dp.ps" /> 106 <output name="stdout" file="test_predict.out" />
127 <param name="reference" value="test_reference.txt" /> 107 </test>
128 108 <test>
129 <output name="stdout" file="test_predict.out" /> 109 <param name="mea_parameter_selector" value="default" />
130 </test> 110 <param name="predict_selector" value="compare" />
131 111 <param name="compare_selector" value="compare" />
132 <test> 112 <param name="structure" value=".....(((.((((((..((......))....)))))).)))......(((((.(((.....(((....))).........).)).))).))..." />
133 <param name="mea_parameter_selector" value="default" /> 113 <param name="reference" value=".....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))" />
134 <param name="predict_selector" value="compare" /> 114 <output name="stdout" file="test_compare.out" />
135 <param name="compare_selector" value="true" /> 115 </test>
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> 116 </tests>
143
144
145 <help><![CDATA[ 117 <help><![CDATA[
146 ===== 118 =====
147 MEA 119 MEA
148 ===== 120 =====
149 121
150 MEA predicts RNA maximum expected accuracy structures from RNA base 122 `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
151 pair probabilities and optionally compares them to a reference
152 structure. In a special mode it skips the prediction and compares a
153 given structure to the reference. For the prediction, MEA allows to 123 given structure to the reference. For the prediction, MEA allows to
154 penalize long base pairs, using parameters alpha, beta, gamma, and 124 penalize long base pairs, using parameters alpha, beta, gamma, and
155 delta. For the comparison of secondary structures, several measures 125 delta. For the comparison of secondary structures, several measures
156 are computed from the confusion matrix of the RNA base pairs. 126 are computed from the confusion matrix of the RNA base pairs.
157 127
186 156
187 * FN = # false negatives 157 * FN = # false negatives
188 158
189 * TN = # true negatives 159 * TN = # true negatives
190 160
191 * SENS = TP/(TP+FN) 'Sensitivity' 161 * SENS = TP/(TP+FN) 'Sensitivity'http://www.bioinf.uni-leipzig.de/Software/mea/
192 162
193 * PPV = TP/(TP+FP) 'Positive Predictive Value' 163 * PPV = TP/(TP+FP) 'Positive Predictive Value'
194 164
195 * F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise 'F1-score' 165 * F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise 'F1-score'
196 166
199 169
200 Special rules for prediction evaluation: 170 Special rules for prediction evaluation:
201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 172
203 * Slide rule: tolerate shift of one base pair end by one base. This 173 * Slide rule: tolerate shift of one base pair end by one base. This
204 rule directly affects the number of true positives. 174 rule directly affects the number of true positives.
175 * Conflict rule: predicted base pairs are false only if they
176 conflict with the reference; two base pair conflict if and only if
177 they share one end This rule directly affects the number of false
178 positives.
205 179
206 * Conflict rule: predicted base pairs are false only if they
207 conflict with the reference; two base pair conflict if and only if
208 they share one end This rule directly affects the number of false
209 positives.
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/
218 ]]></help> 180 ]]></help>
219 <citations> 181 <citations>
220 <citation type="doi">10.1007/978-3-319-02624-4_1</citation> 182 <citation type="doi">10.1007/978-3-319-02624-4_1</citation>
221 </citations> 183 </citations>
222
223 </tool> 184 </tool>