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comparison rnaduplex.xml @ 0:204093ddb00a draft

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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 12:33:48 -0500
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1 <tool id="viennarna_rnaduplex" name="@EXECUTABLE@" version="@VERSION@.0">
2 <description>Compute the structure upon hybridization of two RNA strands</description>
3 <macros>
4 <token name="@EXECUTABLE@">RNAduplex</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 RNAduplex < '$input' > '$tabularFile'
13 -T$temperature -d$dangling --deltaEnergy=$denergy
14 #if $varExists('$advancedOptions.noconversion')
15 $advancedOptions.noconversion
16 $advancedOptions.noLP
17 $advancedOptions.noGU
18 $advancedOptions.noClosingGU
19 $advancedOptions.noTetra
20 #if $advancedOptions.nsp
21 --nsp='$advancedOptions.nsp'
22 #end if
23 #end if
24 ]]>
25 </command>
26 <inputs>
27 <param format="fasta" name="input" type="data" label="Fasta file"/>
28 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
29 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
30 <option value="0">0: ignore dangling ends</option>
31 <option value="1">1: unpaired bases participate in one dangling end only</option>
32 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
33 <option value="3">3: allow coaxial stacking</option>
34 </param>
35 <param argument="--denergy" type="float" value="0.0" label="delta energy range [kcal/mol] for suboptimal structures" help=""/>
36 <param argument="--sorted" type="boolean" truevalue="--sorted" falsevalue="" checked="false" label="Sort by energy" help=""/>
37 <conditional name="advancedOptions">
38 <param name="advancedSelector" type="select" label="advanced options">
39 <option value="basic">basic Options</option>
40 <option value="advanced">advanced Options</option>
41 </param>
42 <when value="advanced">
43 <param argument="--noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences"/>
44 <param argument="--noLP" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help=""/>
45 <param argument="--noGU" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="Allow pairing of G and U at the ends of helices."/>
46 <param argument="--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."/>
47 <param argument="--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."/>
48 <param argument="--nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs."
49 help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy."/>
50 </when>
51 <when value="basic">
52 </when>
53 </conditional>
54 </inputs>
55 <outputs>
56 <data format="txt" name="tabularFile"/>
57 </outputs>
58 <tests>
59 <test>
60 <param name="input" value="rnaduplex_input1.fa"/>
61 <output name="out_file" file="rnaduplex_result1.txt"/>
62 </test>
63 </tests>
64 <help>
65 <![CDATA[
66 **RNAduplex**
67 RNA duplex reads two RNA sequences and computes optimal and suboptimal secondary structures for their hybridization. The calculation is simplified by allowing only inter−molecular base pairs, for the general case use RNAcofold. The computed optimal and suboptimal structure are written to stdout, one structure per line. Suboptimal structures are computed with energy in a certain range of the optimum (kcal/mol). Default is calculation of mfe structure only.
68
69 -----
70
71 **Input format**
72
73 RNAduplex requires one input file in Fasta format. The secondary strucures will be calculated pairwise: 1st sequence with 2nd sequence, 3rd sequence with 4th sequence, etc.
74
75 ------
76
77 **Outputs**
78
79 Each line consist of: The structure in dot bracket format with a "&" separating the two strands. The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. The format is especially useful for computing the hybrid structure between a small probe sequence and a long target sequence.
80
81
82 ]]>
83 </help>
84 <expand macro="citations" />
85 </tool>