Mercurial > repos > rnateam > mea

annotate mea.xml @ 2:34fc6f78ed7c 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 10:13:10 -0400
parents a041bcbb77fc
children 8c457c7a7bd7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
a041bcbb77fc planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents: 0
diff changeset
1 <tool id="mea" name="MEA" version="0.6.4.0">
0
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
2 <description>Predict maximum expected accuracy secondary structures
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
3 of RNAs and compare RNA secondary structures</description>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
4
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
5 <requirements>
1
a041bcbb77fc planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents: 0
diff changeset
6 <requirement type="package" version="2.22.6" >gengetopt</requirement>
a041bcbb77fc planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents: 0
diff changeset
7 <requirement type="package" version="0.6.4" >mea</requirement>
0
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
8 </requirements>
1
a041bcbb77fc planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents: 0
diff changeset
9
0
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
10 <stdio>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
11 <exit_code range="1:" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
12 </stdio>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
13
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
14 <command><![CDATA[
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
15 mea
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
16 #if str($mode.mode_selector) == "predict"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
17 $mode.dotplot
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
18 #else
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
19 --structure `cat $mode.structure`
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
20 #end if
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
21 #if str($reference) != ""
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
22 --reference `cat $reference`
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
23 #end if
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
24 --alpha $mode.alpha
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
25 --beta $mode.beta
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
26 --gamma $mode.gamma
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
27 --delta $mode.delta
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
28 $slide_rule
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
29 $conflict_rule
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
30 > $stdout
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
31 ]]></command>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
32
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
33 <inputs>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
34 <conditional name="mode">
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
35 <param name="mode_selector" type="select" label="Working Mode">
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
36 <option value="predict">Predict</option>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
37 <option value="compare">Compare</option>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
38 </param>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
39 <when value="predict">
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
40 <param name="dotplot" type="data" format="rna_eps" label="Dotplot"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
41 optional="false" help="Dotplot file (RNA base pair probabilities)"/>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
42 <param name="alpha" label="Alpha" type="float"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
43 optional="false" value="0.012"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
44 help="Slope of base pair distance penalty"/>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
45 <param name="beta" label="Beta" type="float"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
46 optional="false" value="315"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
47 help="Turning point of base pair distance penalty" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
48 <param name="gamma" label="Gamma" type="float"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
49 optional="false" value="0.5"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
50 help="Base pair weight factor" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
51 <param name="delta" label="Delta" type="float"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
52 optional="false" value="0.003"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
53 help="Minimum penalty factor for base pairs" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
54 </when>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
55 <when value="compare">
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
56 <param name="structure" format="txt" type="data" label="Structure"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
57 optional="false" help="(Predicted) RNA secondary structure" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
58 </when>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
59 </conditional>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
60
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
61 <param name="reference" format="txt" type="data" label="Reference" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
62
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
63 <param name="slide_rule" label="Slide Rule" type="boolean"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
64 optional="false"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
65 checked="yes"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
66 falsevalue="--no-slide-rule" truevalue=""
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
67 help="Use slide rule" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
68 <param name="conflict_rule" label="Conflict Rule" type="boolean"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
69 optional="false"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
70 checked="yes"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
71 falsevalue="--no-conflict-rule" truevalue=""
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
72 help="Use onflict rule"/>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
73 </inputs>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
74
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
75 <outputs>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
76 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
77 </outputs>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
78
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
79 <tests>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
80 <test>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
81 <param name="alpha"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
82 value="0.012" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
83 <param name="beta"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
84 value="315" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
85 <param name="gamma"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
86 value="0.5" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
87 <param name="delta"
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
88 value="0.003" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
89 <param name="slide-rule" checked="yes" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
90 <param name="conflict-rule" checked="yes" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
91
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
92 <param name="mode_selector" value="predict" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
93 <param name="reference" value="test_reference.txt" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
94
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
95 <param name="dotplot" value="test_dp.ps" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
96
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
97 <output name="stdout" file="test_predict.out" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
98 </test>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
99
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
100 <test>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
101 <param name="mode_selector" value="compare" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
102 <param name="structure" value="test_structure.txt" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
103 <param name="reference" value="test_reference.txt" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
104 <param name="slide-rule" checked="yes" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
105 <param name="conflict-rule" checked="yes" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
106
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
107 <output name="stdout" file="test_compare.out" />
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
108 </test>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
109 </tests>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
110
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
111
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
112 <help><![CDATA[
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
113 ===
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
114 MEA
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
115 ===
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
116
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
117 MEA predicts RNA maximum expected accuracy structures from RNA base
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
118 pair probabilities and optionally compares them to a reference
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
119 structure. In a special mode it skips the prediction and compares a
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
120 given structure to the reference. For the prediction, MEA allows to
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
121 penalize long base pairs, using parameters alpha, beta, gamma, and
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
122 delta. For the comparison of secondary structures, several measures
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
123 are computed from the confusion matrix of the RNA base pairs.
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
124
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
125 ------
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
126 Inputs
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
127 ------
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
128
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
129 The tool accepts dot plot files as generated by RNAfold -p.
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
130
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
131 For (predicted) structure and reference, the tool accepts
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
132 dot-bracket structures with pseudoknots (supporting bracket pairs
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
133 (),{},[],<>,Aa,Bb,...)
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
134
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
135 -------
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
136 Outputs
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
137 -------
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
138
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
139 If predicting a structure, the tool outputs the sequence and the
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
140 predicted dot bracket strucuture with computed score in parenthesis
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
141 following the structure. This mimicks the output of the Vienna
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
142 tools.
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
143
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
144 The result of structure comparison is reported as a line of numbers
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
145
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
146 TP FP FN TN SENS PPV F1 MCC
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
147
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
148 where
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
149
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
150 * TP = # true positives
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
151
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
152 * FP = # false positives
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
153
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
154 * FN = # false negatives
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
155
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
156 * TN = # true negatives
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
157
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
158 * SENS = TP/(TP+FN) 'Sensitivity'
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
159
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
160 * PPV = TP/(TP+FP) 'Positive Predictive Value'
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
161
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
162 * F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise 'F1-score'
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
163
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
164 * MCC = (TP*TN - FP*FN) / sqrt( (TP+FP)*(TP+FN)*(TN+FP)*(TN+FN) ) 'Mathews correlation coefficient'
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
165
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
166
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
167 Special rules for prediction evaluation:
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
168 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
169
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
170 * Slide rule: tolerate shift of one base pair end by one base. This
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
171 rule directly affects the number of true positives.
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
172
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
173 * Conflict rule: predicted base pairs are false only if they
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
174 conflict with the reference; two base pair conflict if and only if
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
175 they share one end This rule directly affects the number of false
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
176 positives.
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
177
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
178 --------
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
179 Download
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
180 --------
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
181
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
182 The command line tool MEA is free software available for download and
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
183 local installation at
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
184 .. __: http://www.bioinf.uni-leipzig.de/Software/mea/
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
185
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
186 ]]></help>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
187 <citations>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
188 <citation type="doi">10.1007/978-3-319-02624-4_1</citation>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
189 </citations>
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
190
9ab890b4d814 planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
rnateam
parents:
diff changeset
191 </tool>