|
0
|
1 <tool id="rnafold" name="RNAfold" version="2.1.6.0">
|
|
|
2 <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>
|
|
|
3 <expand macro="requirements" />
|
|
|
4 <expand macro="version_command" />
|
|
|
5 <expand macro="stdio" />
|
|
|
6 <macros>
|
|
|
7 <token name="@EXECUTABLE@">RNAfold</token>
|
|
|
8 <import>macros.xml</import>
|
|
|
9 </macros>
|
|
|
10 <command>
|
|
|
11 <![CDATA[
|
|
|
12 RNAfold
|
|
|
13 -T $temperature
|
|
|
14 --dangles=$dangling
|
|
|
15 #if $measelect.mea == "yes":
|
|
|
16 --MEA=$measelect.meavalue
|
|
|
17 #else
|
|
|
18 $measelect.pf
|
|
|
19 #end if
|
|
|
20 #if $varExists('$advancedOptions.nogu'):
|
|
|
21 $advancedOptions.noconversion
|
|
|
22 $advancedOptions.gquad
|
|
|
23 $advancedOptions.nolp
|
|
|
24 $advancedOptions.nogu
|
|
|
25 $advancedOptions.noclosinggu
|
|
|
26 $advancedOptions.canonicalonly
|
|
|
27 $advancedOptions.circular
|
|
|
28 #end if
|
|
|
29
|
|
|
30 < $fasta_input
|
|
|
31
|
|
|
32 > $tabular_file
|
|
|
33 ]]>
|
|
|
34 </command>
|
|
|
35
|
|
|
36 <inputs>
|
|
|
37 <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
|
|
|
38 <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
|
|
|
39 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
|
|
|
40 <option value="0">0: ignore dangling ends</option>
|
|
|
41 <option value="1">1: unpaired bases participate in one dangling end only</option>
|
|
|
42 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
|
|
|
43 <option value="3">3: allow coaxial stacking</option>
|
|
|
44 </param>
|
|
|
45 <conditional name="measelect">
|
|
|
46 <param name="mea" type="select" label="Calculate Maximum Expected accuracy" help="--MEA">
|
|
|
47 <option value="no">No</option>
|
|
|
48 <option value="yes">Yes</option>
|
|
|
49 </param>
|
|
|
50 <when value="yes">
|
|
|
51 <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/>
|
|
|
52 </when>
|
|
|
53 <when value="no">
|
|
|
54 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
|
|
|
55 </when>
|
|
|
56 </conditional>
|
|
|
57 <conditional name="advancedOptions">
|
|
|
58 <param name="advancedSelector" type="boolean" checked="false" label=" advanced options"/>
|
|
|
59 <when value="true">
|
|
|
60 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/>
|
|
|
61 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/>
|
|
|
62 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/>
|
|
|
63 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/> <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
|
|
|
64 <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/>
|
|
|
65 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
|
|
|
66 </when>
|
|
|
67 </conditional>
|
|
|
68 </inputs>
|
|
|
69 <outputs>
|
|
|
70 <data format="tabular" name="tabular_file"/>
|
|
|
71 <data format="txt" name="structure">
|
|
|
72 <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" visible="true"/>
|
|
|
73 </data>
|
|
|
74 <data format="txt" name="dotplot">
|
|
|
75 <filter>measelect['pf'] is True</filter>
|
|
|
76 <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/>
|
|
|
77 </data>
|
|
|
78 </outputs>
|
|
|
79 <tests>
|
|
|
80 </tests>
|
|
|
81 <help>
|
|
|
82 <![CDATA[
|
|
|
83 **RNAfold**
|
|
|
84
|
|
|
85 The program reads RNA sequences, calculates their minimum free
|
|
|
86 energy (mfe) structure and the mfe structure in dot-bracket notation.
|
|
|
87
|
|
|
88 If the -p option was given it also computes the
|
|
|
89 partition function (pf) and base pairing probability matrix.
|
|
|
90
|
|
|
91 The dot plot of the base pairing probability matrix shows a matrix of squares with area proportional to the pairing
|
|
|
92 probability in the upper right half, and one square for each pair in the
|
|
|
93 minimum free energy structure in the lower left half. For each pair i-j with
|
|
|
94 probability p>10E-6 there is a line of the form
|
|
|
95
|
|
|
96 i j sqrt(p) ubox
|
|
|
97
|
|
|
98 in the PostScript file, so that the pair probabilities can be easily extracted.
|
|
|
99
|
|
|
100 The sequences have to be provided in FASTA format. The first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively.
|
|
|
101 The program will read the whole FASTA input file and provide output for each found sequence.
|
|
|
102
|
|
|
103
|
|
|
104 -----
|
|
|
105
|
|
|
106 **Input format**
|
|
|
107
|
|
|
108 RNAfold requires one input file
|
|
|
109 - FASTA file
|
|
|
110
|
|
|
111 ------
|
|
|
112
|
|
|
113 **Outputs**
|
|
|
114
|
|
|
115 - Secondary structures in dot-bracket notation
|
|
|
116
|
|
|
117 - several possible postscript images bundled together in a tar file
|
|
|
118 - secondary structure for each sequence in the input file
|
|
|
119 - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence
|
|
|
120
|
|
|
121 ]]>
|
|
|
122 </help>
|
|
|
123 <expand macro="citations" />
|
|
|
124 </tool>
|
