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comparison kinwalker.xml @ 1:643da63cb382 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
author | rnateam |
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date | Wed, 12 Jul 2017 14:10:44 -0400 |
parents | cb66f1d643e4 |
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1 <tool id="rbc_kinwalker" name="Kinwalker" version="1.0"> | |
2 <description> | |
3 <![CDATA[ | |
4 cotranscriptional folding of RNAs | |
5 ]]> | |
6 </description> | |
7 <requirements> | |
8 <requirement type="package" version="1.0">kinwalker</requirement> | |
9 <requirement type="package" version="8.22">gnu_coreutils</requirement> | |
10 <requirement type="package" version="2.1">vienna_rna</requirement> | |
11 </requirements> | |
12 <command> | |
13 <![CDATA[ | |
14 head -n 1 $input_sequence | head -c -1 -q > seq.ident | |
15 && | |
16 sed '1d' $input_sequence > input.seq | |
17 && | |
18 kinwalker | |
19 $init_structure | |
20 $interrupt | |
21 ##$printfront | |
22 | |
23 --barrier_heuristic $barrier_heuristic.used | |
24 | |
25 #if $barrier_heuristic.used == "M" | |
26 --grouping $barrier_heuristic.grouping | |
27 --lookahead $barrier_heuristic.lookahead | |
28 #else if $barrier_heuristic.used == "B" | |
29 --maxkeep $barrier_heuristic.maxkeep | |
30 #end if | |
31 | |
32 --dangle $dangle | |
33 --noLonelyPairs $noLonelyPairs | |
34 --transcribed $transcribed | |
35 --transcription_rate $transcription_rate | |
36 --windowsize $windowsize | |
37 | |
38 < input.seq | |
39 | |
40 > blah | |
41 | |
42 && | |
43 sed -n '2s/[\.\(\)]\+\s\+\(.\+\)$/ mfe: \1/p' blah > energy | |
44 | |
45 && | |
46 cat seq.ident energy > $mfe_struct | |
47 | |
48 && | |
49 sed -e '2s/^\([\.\(\)]\+\).*$/\1/' -ne '1,2p' blah >> $mfe_struct | |
50 | |
51 && | |
52 sed -e 's/[ \t]*$//' -ne '/TRAJ/,/Kinwal/ {/TRAJ/n;/Kinwal/!{s/\s/\t/gp}}' blah > $trajectory | |
53 ]]> | |
54 </command> | |
55 <stdio> | |
56 <!-- Anything other than zero is an error --> | |
57 <exit_code range="1:" /> | |
58 <exit_code range=":-1" /> | |
59 <!-- In case the return code has not been set propery check stderr too --> | |
60 <regex match="Error:" /> | |
61 <regex match="Exception:" /> | |
62 </stdio> | |
63 <inputs> | |
64 <param name="input_sequence" format="fasta" type="data" label="Input sequence" help="A single sequence in FASTA format"/> | |
65 <param name="init_structure" type="boolean" truevalue="--init_structure" falsevalue="" checked="false" label="Start with a structure other than the open chain" help="(--init_structure)"/> | |
66 <param name="interrupt" type="boolean" truevalue="--interrupt" falsevalue="" checked="false" label="Allow interrupted folding trajectories when the barrier is exceeded" help="(--interrupt)"/> | |
67 <!-- need to implement with dataset collections <param name="printfront" type="boolean" truevalue="!doublehypen!printfront" falsevalue="" checked="true" label="Creates PS plots of front progression" help="(!doublehypen!printfront)"/> --> | |
68 <conditional name="barrier_heuristic"> | |
69 <param name="used" type="select" label="Barrier Heuristic" help="(--barrier_heuristic)"> | |
70 <option value="M" selected="true">Morgan-Higgs</option> | |
71 <option value="S">Limit small stacks</option> | |
72 <option value="B">Barriers</option> | |
73 <option value="A">All</option> | |
74 </param> | |
75 <when value="M"> | |
76 <param name="grouping" type="select" label="How to treat conflict groups" help="(--grouping)"> | |
77 <option value="standard" selected="true">Standard</option> | |
78 <option value="regroup">Re-group</option> | |
79 </param> | |
80 <param name="lookahead" type="integer" value="1" label="Number of basepairs that MorganHiggs forms its subpaths from" help="(--lookahead)"/> | |
81 </when> | |
82 <when value="S" /> | |
83 <when value="B"> | |
84 <param name="maxkeep" type="integer" value="1" label="Breadth of breadth first search" help="(--maxkeep)"/> | |
85 </when> | |
86 <when value="A" /> | |
87 </conditional> | |
88 <param name="dangle" type="select" label="Dangle value as in VienneRNA package" help="(--dangle)"> | |
89 <option value="0" selected="true">0</option> | |
90 <option value="1">1</option> | |
91 <option value="2">2</option> | |
92 </param> | |
93 <param name="noLonelyPairs" type="integer" value="2" label="Value of noLonelyPairs as in ViennaRNA" help="(--noLonelyPairs)"/> | |
94 | |
95 <param name="transcribed" type="integer" value="1" label="Number of bases initially transcribed" help="0 means all is transcribed (--transcribed)"/> | |
96 <param name="transcription_rate" type="float" value="200" label="Number of bases transcribed per second" help="(--transcription_rate)"/> | |
97 <param name="windowsize" type="integer" value="0" label="Max size of substructures considered for folding events during transcription" help="0= all are considered. (--windowsize)"/> | |
98 </inputs> | |
99 <outputs> | |
100 <data format="fasta" name="mfe_struct" label="MFE structure from ${tool.name} on ${on_string}" /> | |
101 <data format="tabular" name="trajectory" label="Trajectory of ${tool.name} on ${on_string}" /> | |
102 </outputs> | |
103 <tests> | |
104 <test> | |
105 <param name="input_sequence" value="test_sequence_input.fasta" /> | |
106 <param name="init_structure" value="" /> | |
107 <param name="interrupt" value="" /> | |
108 <param name="used" value="M" /> | |
109 <param name="grouping" value="standard" /> | |
110 <param name="lookahead" value="1" /> | |
111 <param name="dangle" value="0" /> | |
112 <param name="noLonelyPairs" value="2" /> | |
113 <param name="transcribed" value="1" /> | |
114 <param name="transcription_rate" value="200" /> | |
115 <param name="windowsize" value="0" /> | |
116 <output name="mfe_struct" file="mfe_struct_result.fasta" /> | |
117 <output name="trajectory" file="trajectory_result.tabular" /> | |
118 </test> | |
119 </tests> | |
120 <help> | |
121 <![CDATA[ | |
122 **What Kinwalker does** | |
123 | |
124 Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. | |
125 In each transcription event one base from the RNA sequence is appended to the already transcribed and (partially) folded subsequence. | |
126 Kinwalker executes transcription events at regular time intervals. In each folding event a subsequence of the already transcribed | |
127 RNA sequence is selected and a new structure is formed by combining base pairs from the current structure with base pairs from the | |
128 mfE structure of that subsequence. | |
129 | |
130 This is done in such a way that the new structure includes base pairs from both structures in an energetically favorable manner. | |
131 Kinwalker estimates the waiting times for individual folding events depending on the height of the energy barrier between the | |
132 current structure and the new structure into which the molecule is folded. Folding events between structures can only occur, | |
133 if the energy barrier between them is less than the maximum allowed energy barrier. | |
134 | |
135 As folding paths can only be calculated exhaustively for short sequences (n>100), heuristic approaches have to be employed which explicitly | |
136 construct a (re)folding path between the two structures. The saddle height is then estimated as the highest point along the path. | |
137 The best known algorithm for approximating saddle heights between RNA conformations is the Morgan-Higgs heuristic, | |
138 which tries to find a folding path from an origin secondary structure to a target secondary structure where the maximum height | |
139 along the path is minimal. The heuristic models state transitions at base pair resolution. | |
140 ]]> | |
141 </help> | |
142 <citations> | |
143 <citation type="doi">10.1016/j.jmb.2008.02.064</citation> | |
144 </citations> | |
145 </tool> |