Mercurial > repos > rnateam > mea

comparison mea.xml @ 0:9ab890b4d814 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
author rnateam
date Wed, 01 Jul 2015 09:56:14 -0400
parents
children a041bcbb77fc
comparison
equal deleted inserted replaced
-1:000000000000 0:9ab890b4d814
1 <tool id="mea" name="MEA" version="0.6.4">
2 <description>Predict maximum expected accuracy secondary structures
3 of RNAs and compare RNA secondary structures</description>
4
5 <requirements>
6
7 </requirements>
8 <stdio>
9 <exit_code range="1:" />
10 </stdio>
11
12 <command><![CDATA[
13 mea
14 #if str($mode.mode_selector) == "predict"
15 $mode.dotplot
16 #else
17 --structure `cat $mode.structure`
18 #end if
19 #if str($reference) != ""
20 --reference `cat $reference`
21 #end if
22 --alpha $mode.alpha
23 --beta $mode.beta
24 --gamma $mode.gamma
25 --delta $mode.delta
26 $slide_rule
27 $conflict_rule
28 > $stdout
29 ]]></command>
30
31 <inputs>
32 <conditional name="mode">
33 <param name="mode_selector" type="select" label="Working Mode">
34 <option value="predict">Predict</option>
35 <option value="compare">Compare</option>
36 </param>
37 <when value="predict">
38 <param name="dotplot" type="data" format="rna_eps" label="Dotplot"
39 optional="false" help="Dotplot file (RNA base pair probabilities)"/>
40 <param name="alpha" label="Alpha" type="float"
41 optional="false" value="0.012"
42 help="Slope of base pair distance penalty"/>
43 <param name="beta" label="Beta" type="float"
44 optional="false" value="315"
45 help="Turning point of base pair distance penalty" />
46 <param name="gamma" label="Gamma" type="float"
47 optional="false" value="0.5"
48 help="Base pair weight factor" />
49 <param name="delta" label="Delta" type="float"
50 optional="false" value="0.003"
51 help="Minimum penalty factor for base pairs" />
52 </when>
53 <when value="compare">
54 <param name="structure" format="txt" type="data" label="Structure"
55 optional="false" help="(Predicted) RNA secondary structure" />
56 </when>
57 </conditional>
58
59 <param name="reference" format="txt" type="data" label="Reference" />
60
61 <param name="slide_rule" label="Slide Rule" type="boolean"
62 optional="false"
63 checked="yes"
64 falsevalue="--no-slide-rule" truevalue=""
65 help="Use slide rule" />
66 <param name="conflict_rule" label="Conflict Rule" type="boolean"
67 optional="false"
68 checked="yes"
69 falsevalue="--no-conflict-rule" truevalue=""
70 help="Use onflict rule"/>
71 </inputs>
72
73 <outputs>
74 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
75 </outputs>
76
77 <tests>
78 <test>
79 <param name="alpha"
80 value="0.012" />
81 <param name="beta"
82 value="315" />
83 <param name="gamma"
84 value="0.5" />
85 <param name="delta"
86 value="0.003" />
87 <param name="slide-rule" checked="yes" />
88 <param name="conflict-rule" checked="yes" />
89
90 <param name="mode_selector" value="predict" />
91 <param name="reference" value="test_reference.txt" />
92
93 <param name="dotplot" value="test_dp.ps" />
94
95 <output name="stdout" file="test_predict.out" />
96 </test>
97
98 <test>
99 <param name="mode_selector" value="compare" />
100 <param name="structure" value="test_structure.txt" />
101 <param name="reference" value="test_reference.txt" />
102 <param name="slide-rule" checked="yes" />
103 <param name="conflict-rule" checked="yes" />
104
105 <output name="stdout" file="test_compare.out" />
106 </test>
107 </tests>
108
109
110 <help><![CDATA[
111 ===
112 MEA
113 ===
114
115 MEA predicts RNA maximum expected accuracy structures from RNA base
116 pair probabilities and optionally compares them to a reference
117 structure. In a special mode it skips the prediction and compares a
118 given structure to the reference. For the prediction, MEA allows to
119 penalize long base pairs, using parameters alpha, beta, gamma, and
120 delta. For the comparison of secondary structures, several measures
121 are computed from the confusion matrix of the RNA base pairs.
122
123 ------
124 Inputs
125 ------
126
127 The tool accepts dot plot files as generated by RNAfold -p.
128
129 For (predicted) structure and reference, the tool accepts
130 dot-bracket structures with pseudoknots (supporting bracket pairs
131 (),{},[],<>,Aa,Bb,...)
132
133 -------
134 Outputs
135 -------
136
137 If predicting a structure, the tool outputs the sequence and the
138 predicted dot bracket strucuture with computed score in parenthesis
139 following the structure. This mimicks the output of the Vienna
140 tools.
141
142 The result of structure comparison is reported as a line of numbers
143
144 TP FP FN TN SENS PPV F1 MCC
145
146 where
147
148 * TP = # true positives
149
150 * FP = # false positives
151
152 * FN = # false negatives
153
154 * TN = # true negatives
155
156 * SENS = TP/(TP+FN) 'Sensitivity'
157
158 * PPV = TP/(TP+FP) 'Positive Predictive Value'
159
160 * F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise 'F1-score'
161
162 * MCC = (TP*TN - FP*FN) / sqrt( (TP+FP)*(TP+FN)*(TN+FP)*(TN+FN) ) 'Mathews correlation coefficient'
163
164
165 Special rules for prediction evaluation:
166 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
167
168 * Slide rule: tolerate shift of one base pair end by one base. This
169 rule directly affects the number of true positives.
170
171 * Conflict rule: predicted base pairs are false only if they
172 conflict with the reference; two base pair conflict if and only if
173 they share one end This rule directly affects the number of false
174 positives.
175
176 --------
177 Download
178 --------
179
180 The command line tool MEA is free software available for download and
181 local installation at
182 .. __: http://www.bioinf.uni-leipzig.de/Software/mea/
183
184 ]]></help>
185 <citations>
186 <citation type="doi">10.1007/978-3-319-02624-4_1</citation>
187 </citations>
188
189 </tool>