Mercurial > repos > rnateam > viennarna_rna2dfold

comparison rna2dfold.xml @ 0:0373277da3ec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author rnateam
date Tue, 06 Dec 2016 12:36:38 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:0373277da3ec
1 <tool id="viennarna_rna2dfold" name="@EXECUTABLE@" version="@VERSION@.0">
2 <description>explore structure space between two reference structures</description>
3 <macros>
4 <token name="@EXECUTABLE@">RNA2Dfold</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
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 $noBT
20 $advancedOptions.noconversion
21 $advancedOptions.noclosinggu
22 $advancedOptions.notetra
23 $advancedOptions.circ
24 #if $varExists('$advancedOptions.maxK')
25 --maxDist1=$advancedOptions.maxK
26 --maxDist2=$advancedOptions.maxL
27 #end if
28 < '$custom_input' > '$out_file'
29 ]]>
30 </command>
31 <inputs>
32 <param format="txt,dbn" name="custom_input" type="data" label="Custom File"/>
33 <param name="temperature" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
34 <param name="nrbt" type="integer" value="1" label="Number of backtrack of Boltzmann samples" help="--stochBT=INT"/>
35 <param name="nk" type="integer" value="-1" label="[k]: Distance to first reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/>
36 <param name="nl" type="integer" value="-1" label="[l]: Distance to second reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/>
37 <param name="dangling" type="select" label="How to treat dangling end energies" help="-d">
38 <option value="2" selected="true">Unpaired bases participate in all dangling ends (2)</option>
39 <option value="0">Ignore dangling ends (0)</option>
40 </param>
41 <param name="noBT" type="boolean" checked="true" truevalue="" falsevalue="--noBT"
42 label="Backtrack structures, don't calculate energy contributions only" argument="--noBT"/>
43 <conditional name="pfselect">
44 <param name="pf" type="select" label="Calculate partition function" help="--partfunc">
45 <option value="no">no</option>
46 <option value="yes">yes</option>
47 </param>
48 <when value="yes">
49 <param name="pfscaling" type="float" value="1.0" label="Scaling factor for the partition function"/>
50 </when>
51 <when value="no">
52 </when>
53 </conditional>
54 <section name="advancedOptions" title="Advanced options">
55 <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>
56 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
57 <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/>
58 <param argument="--circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Model as circular RNA structure"/>
59 <param name="maxK" type="integer" value="10" max="44" label="Maximum distance to first reference structure" argument="--maxDist1"/>
60 <param name="maxL" type="integer" value="10" max="43" label="Maximum distance to second reference structure" argument="--maxDist2"/>
61 <!-- This argument causes "Segmentation fault"-->
62 <!-- <param name="nogu" type="boolean" truevalue="" falsevalue="- -noGU" checked="true" label="Allow GU pairing" help="Allow wobbly pairs G-U."/> -->
63 </section>
64 </inputs>
65 <outputs>
66 <data format="dbn" name="out_file"/>
67 </outputs>
68 <tests>
69 <test>
70 <param name="custom_input" value="rna2dfold_input1.txt"/>
71 <param name="nrbt" value="0"/>
72 <output name="out_file1" file="rna2dfold_result1.txt"/>
73 </test>
74 </tests>
75 <help>
76 <![CDATA[
77 **RNA2Dfold**
78
79 The program partitions the secondary structure space into (basepair)distance
80 classes according to two fixed reference structures. It expects a sequence and
81 two secondary structures in dot-bracket notation as its inputs. For each
82 distance class, the MFE representative, Boltzmann probabilities and Gibbs free
83 energy is computed. Additionally, a stochastic backtracking routine allows to
84 produce samples of representative suboptimal secondary structures from each
85 partition.
86 The k-distance corresponds to the distance to the first reference structure, and
87 the l-distance corresponds to the distance to the second reference structure
88
89 -----
90
91 **Input format**
92
93 RNA2Dfold requires one input file in the following format
94
95 - 1st line: RNA sequence
96 - 2nd line: first reference structure in dot-bracket format
97 - 3rd line: second reference structure in dot-bracket format
98
99 ------
100
101 **Outputs**
102
103 - text output with several secondary structures and its energies
104
105 ]]>
106 </help>
107 <expand macro="citations" />
108 </tool>