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comparison rnalfold.xml @ 0:a59547093b10 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 12:31:55 -0500
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-1:000000000000 0:a59547093b10
1 <tool id="viennarna_rnalfold" name="@EXECUTABLE@" version="@VERSION@.0">
2 <description>calculates locally stable secondary structures of RNA</description>
3
4 <macros>
5 <token name="@EXECUTABLE@">RNALfold</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 RNALfold -L $span -T $temperature -d$dangling < '$fasta_input'
14 #if $varExists('$advancedOptions.noconversion')
15 $advancedOptions.noconversion
16 $advancedOptions.gquad
17 $advancedOptions.nolp
18 $advancedOptions.nogu
19 $advancedOptions.noclosinggu
20 $advancedOptions.notetra
21 #if $advancedOptions.activateZscore
22 #if str($advancedOptions.zscore) <> ""
23 --zscore=$advancedOptions.zscore
24 #else
25 --zscore
26 #end if
27 #end if
28 #end if
29 | sed -r 's/(^[.()]*) +(\(.*\)) +(.*)/\1\t\2\t\3/' > '$out_file'
30 ]]>
31 </command>
32 <inputs>
33 <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
34 <param name="span" type="integer" min="0" max="5000" value="150" label="base pair span" help="Maximal distance between two paired bases. (-L)"/>
35 <param name="temperature" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
36 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
37 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
38 <option value="0">ignore dangling ends (0)</option>
39 <option value="1">unpaired bases participate in one dangling end only (1)</option>
40 <option value="3">allow coaxial stacking (3)</option>
41 </param>
42 <conditional name="advancedOptions">
43 <param name="advancedSelector" type="select" label="advanced options">
44 <option value="basic">basic Options</option>
45 <option value="advanced">advanced Options</option>
46 </param>
47 <when value="advanced">
48 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="Take G Quadruplex formation into account" argument="-g"/>
49 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
50 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
51 <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"/>
52 <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)"/>
53 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
54 <param name="activateZscore" type="boolean" checked="false" label="Activate Z−score computation. An optional argument may be supplied to set the threshold" help="(--zscore)"/>
55 <param name="zscore" type="float" value="-2" optional="true" label="Z-score" help="An optional argument may be supplied to set the threshold"/>
56 </when>
57 <when value="basic">
58 </when>
59 </conditional>
60 </inputs>
61 <outputs>
62 <data format="txt" name="out_file"/>
63 </outputs>
64 <tests>
65 <test>
66 <param name="fasta_input" value="rnalfold_input1.fa"/>
67 <output name="out_file" file="rnalfold_result1.txt"/>
68 </test>
69 </tests>
70 <help>
71 <![CDATA[
72 **RNALfold**
73
74 Compute locally stable RNA secondary structure with a maximal base pair span.
75 For a sequence of length n and a base pair span of L the algorithm uses only
76 O(n+L*L) memory and O(n*L*L) CPU time. *Thus it is practical to "scan" very
77 large genomes for short RNA structures*.
78 Output consists of a list of secondary structure components of size <= L, one
79 entry per line. Each output line contains the predicted local structure its
80 energy in kcal/mol and the starting position of the local structure.
81
82 -----
83
84 **Input format**
85
86 - RNALfold requires one input file in FASTA format
87
88 ------
89
90 **Outputs**
91
92 - text output with dot-bracket notation and free energies of the secondary structures
93
94 ]]>
95 </help>
96 <expand macro="citations" />
97 </tool>