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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
author rnateam
date Wed, 20 Dec 2017 08:30:44 -0500
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-1:000000000000 0:22e8485bc5f3
1 <tool id="viennarna_rnaplfold" name="@EXECUTABLE@" version="@VERSION@.0">
2 <description> predicts RNA secondary structures including pseudoknots</description>
3
4 <macros>
5 <token name="@EXECUTABLE@">RNAplfold</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="stdio" />
10 <expand macro="version_command" />
11 <command>
12 <![CDATA[
13 RNAplfold < '$input'
14 -T$temperature
15 --dangles=$dangling
16 --cutoff=$cutoff
17 --winsize=$winsize
18 --span=$span
19 $onthefly
20 $openingenergies
21 #if $varExists('$unpairedOption.ulength')
22 --ulength=$unpairedOption.ulength
23 #end if
24 #if $varExists('$advancedOptions.nolp')
25 $advancedOptions.noconversion
26 $advancedOptions.nolp
27 $advancedOptions.nogu
28 $advancedOptions.noclosinggu
29 $advancedOptions.notetra
30 #end if
31 && find -name '*_basepairs' -or -name '*_lunp' -or -name '*_openen*' > files.tmp
32 && tar -cf '$outputf' --files-from=files.tmp
33
34 ]]>
35 </command>
36
37 <inputs>
38 <param format="fasta" name="input" type="data" label="Fasta file"/>
39 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
40 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
41 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
42 <option value="0">ignore dangling ends (0)</option>
43 <option value="1">unpaired bases participate in one dangling end only (1)</option>
44 <option value="3">allow coaxial stacking (3)</option>
45 </param>
46 <param name="winsize" type="integer" value="70" label="Average pairing probabilities over this windowsize" help="--winsize"/>
47 <param name="span" type="integer" value="70" label="Maximum seperation between base pairs" help="--span, -L"/>
48 <param name="cutoff" type="float" value="0.01" label="Cutoff probability for report on base pairing" help="--cutoff"/>
49 <param name="onthefly" type="boolean" truevalue="--print_onthefly" falsevalue="" checked="false" label="Print simplified base pair probabilities (_basepairs output)" help="--print_onthefly"/>
50 <param name="openingenergies" type="boolean" truevalue="--opening_energies" falsevalue="" checked="false" label="Output in logarithm of the probabilities (_openen output)" help="--opening_energies"/>
51 <param argument="--plex_output" type="boolean" truevalue="--plex_output" falsevalue="" checked="false" label="" help=""/>
52 <conditional name="unpairedOption">
53 <param name="unpairedSelector" type="select" label="Compute probabilty that region is unpaired (_lunp output)">
54 <option value="no" selected="true">no</option>
55 <option value="yes">yes</option>
56 </param>
57 <when value="yes">
58 <param name="ulength" type="integer" value="31" label="Maximal lenght of unpaired region" help="--ulength"/>
59 </when>
60 <when value="no">
61 </when>
62 </conditional>
63 <conditional name="advancedOptions">
64 <param name="advancedSelector" type="select" label="advanced options">
65 <option value="basic">basic Options</option>
66 <option value="advanced">advanced Options</option>
67 </param>
68 <when value="advanced">
69 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
70 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
71 <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"/>
72 <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)"/>
73 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
74 </when>
75 <when value="basic">
76 </when>
77 </conditional>
78 </inputs>
79 <outputs>
80 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
81 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
82 </collection>
83 <data format="tar" name="outputf"/>
84 </outputs>
85 <tests>
86 <test>
87 <param name="input" value="rnaplfold_input1.fa"/>
88 <output_collection name="matrix_outputs" type="list">
89 <element name="Anolis_caro_chrUn_GL343590.trna2-A">
90 <assert_contents>
91 <has_text_matching expression="%%Creator: ViennaRNA-@VERSION@" />
92 </assert_contents>
93 </element>
94 </output_collection>
95 </test>
96 </tests>
97 <help>
98 <![CDATA[
99
100 **RNAplfold**
101
102 Computes local pair probabilities for base pairs with a maximal span of L. The probabilities are averaged over all windows of size L that contain the base pair. For a sequence of length n and a window size of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short stable RNA structures.
103
104
105 -----
106
107 **Input format**
108
109 RNAPplfold requires one input file
110
111 - Fasta file
112
113 ------
114
115 **Outputs**
116
117 For each structure in the Fasta input a postscript image with dot-plot of the pairing probabilities is generated. Different output is generated with the "--ulength", "--print_onthefly" and "--opening_energies" flags.
118 The Dot Plot Matrices are stored in a Postscript file.
119 The other output is packed in a tar file.
120
121
122 ]]>
123 </help>
124 <expand macro="citations" />
125 </tool>