Mercurial > repos > rnateam > vienna_rna
comparison rna2dfold.xml @ 0:78d673470d45 draft
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author | rnateam |
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date | Wed, 04 Feb 2015 12:05:27 -0500 |
parents | |
children | 5e58cbf27a05 |
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-1:000000000000 | 0:78d673470d45 |
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1 <tool id="rna2dfold" name="RNA2Dfold" version="2.1.6.0"> | |
2 <description>explore structure space between two reference structures</description> | |
3 <expand macro="requirements" /> | |
4 <expand macro="version_command" /> | |
5 <expand macro="stdio" /> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">RNA2Dfold</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <command> | |
11 <![CDATA[ | |
12 RNA2Dfold -T $temperature -d $dangling --stochBT=$nrbt | |
13 #if int($nk) > -1 and int($nl) > -1 | |
14 --neighborhood=$nk:$nl | |
15 #end if | |
16 #if $varExists('$pfselect.pfscaling') | |
17 --partfunc --pfScale=$pfselect.pfscaling | |
18 #end if | |
19 #if $varExists('$advancedOptions.noconversion') | |
20 #if $advancedOptions.noconversion | |
21 --noconv | |
22 #end if | |
23 #if $advancedOptions.nogu | |
24 --noGU | |
25 #end if | |
26 #if $advancedOptions.noclosinggu | |
27 --noClosingGU | |
28 #end if | |
29 #if $advancedOptions.notetra | |
30 --noTetra | |
31 #end if | |
32 --maxDist1=$maxK | |
33 --maxDist2=$maxL | |
34 #end if | |
35 < $custom_input > $out_file | |
36 ]]> | |
37 </command> | |
38 <inputs> | |
39 <param format="txt" name="custom_input" type="data" label="Custom File"/> | |
40 <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/> | |
41 <param name="nrbt" type="integer" value="1" label="number of backtrack of Boltzmann samples" help="--stochBT=INT"/> | |
42 <param name="nk" type="integer" value="-1" label="k distance to first reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/> | |
43 <param name="nl" type="integer" value="-1" label="l distance to second reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/> | |
44 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d"> | |
45 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option> | |
46 <option value="0">ignore dangling ends (0)</option> | |
47 <option value="1">unpaired bases participate in one dangling end only (1)</option> | |
48 <option value="3">allow coaxial stacking (3)</option> | |
49 </param> | |
50 <param name="circular" type="boolean" checked="false" label="assume circular RNA structure" help="--circ"/> | |
51 <conditional name="pfselect"> | |
52 <param name="pf" type="select" label="calculate partition function" help="--partfunc"> | |
53 <option value="no">no</option> | |
54 <option value="yes">yes</option> | |
55 </param> | |
56 <when value="yes"> | |
57 <param name="pfscaling" size="6" type="float" value="1.0" label="scaling factor for the partition function"/> | |
58 </when> | |
59 </conditional> | |
60 | |
61 <conditional name="advancedOptions"> | |
62 <param name="advancedSelector" type="select" label="advanced options"> | |
63 <option value="basic">basic Options</option> | |
64 <option value="advanced">advanced Options</option> | |
65 </param> | |
66 <when value="advanced"> | |
67 <param name="maxK" type="integer" value="50" label="Maximum distance to first reference structure" help="--maxDist1=INT"/> | |
68 <param name="maxL" type="integer" value="50" label="Maximum distance to second reference structure" help="--maxDist2=INT"/> | |
69 <param name="noconversion" type="boolean" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/> | |
70 <param name="gquad" type="boolean" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/> | |
71 <param name="nogu" type="boolean" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> | |
72 <param name="noclosinggu" type="boolean" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/> | |
73 <param name="notetra" type="boolean" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/> | |
74 </when> | |
75 </conditional> | |
76 </inputs> | |
77 <outputs> | |
78 <data format="txt" name="out_file"/> | |
79 </outputs> | |
80 <tests> | |
81 </tests> | |
82 <help> | |
83 <![CDATA[ | |
84 **RNA2Dfold** | |
85 | |
86 The program partitions the secondary structure space into (basepair)distance | |
87 classes according to two fixed reference structures. It expects a sequence and | |
88 two secondary structures in dot-bracket notation as its inputs. For each | |
89 distance class, the MFE representative, Boltzmann probabilities and Gibbs free | |
90 energy is computed. Additionally, a stochastic backtracking routine allows to | |
91 produce samples of representative suboptimal secondary structures from each | |
92 partition. | |
93 The k-distance corresponds to the distance to the first reference structure, and | |
94 the l-distance corresponds to the distance to the second reference structure | |
95 | |
96 ----- | |
97 | |
98 **Input format** | |
99 | |
100 RNA2Dfold requires one input file in the following format | |
101 | |
102 - 1st line: RNA sequence | |
103 - 2nd line: first reference structure in dot-bracket format | |
104 - 3rd line: second reference structure in dot-bracket format | |
105 | |
106 ------ | |
107 | |
108 **Outputs** | |
109 | |
110 - text output with several secondary structures and its energies | |
111 | |
112 ]]> | |
113 </help> | |
114 <expand macro="requirements" /> | |
115 </tool> |