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comparison rnalalifold.xml @ 0:19d6a5fa6bcf 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 12:35:00 -0500
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1 <tool id="viennarna_rnalalifold" name="@EXECUTABLE@" version="@VERSION@.0">
2 <description>Calculate locally stable secondary structures for a set of aligned RNAs</description>
3 <macros>
4 <token name="@EXECUTABLE@">RNALalifold</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 RNALalifold '$input' > '$output'
13 -T$temperature -d$dangling
14 -L$span
15 $mis
16 #if $varExists('$advancedOptions.nolp')
17 $advancedOptions.nolp
18 $advancedOptions.nogu
19 $advancedOptions.noclosinggu
20 $advancedOptions.notetra
21 --cfactor=$advancedOptions.cfactor
22 --nfactor=$advancedOptions.nfactor
23 $advancedOptions.ribosum
24 #end if
25 ]]>
26 </command>
27
28 <inputs>
29 <param format="txt" name="input" type="data" label="Clustal file"/>
30 <param name="span" type="integer" min="0" max="5000" value="60" label="base pair span" help="Maximal distance between two paired bases. (-L)"/>
31 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
32 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
33 <option value="0">0: ignore dangling ends</option>
34 <option value="1">1: unpaired bases participate in one dangling end only</option>
35 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
36 <option value="3">3: allow coaxial stacking</option>
37 </param>
38 <!-- the -p option led to segmentation faults with version 2.1.2 and 2.1.7, it was later removed from verion 2.1.10 -->
39 <!--<param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>-->
40 <param name="mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="--mis"/>
41 <conditional name="advancedOptions">
42 <param name="advancedSelector" type="select" label="advanced options">
43 <option value="basic">basic Options</option>
44 <option value="advanced">advanced Options</option>
45 </param>
46 <when value="advanced">
47 <!-- the -cutoff option was removed from version 2.2.10 -->
48 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
49 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
50 <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"/>
51 <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)"/>
52 <param name="cfactor" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
53 <param name="nfactor" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
54 <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
55 </when>
56 <when value="basic">
57 </when>
58 </conditional>
59 </inputs>
60 <outputs>
61 <data format="txt" name="output" />
62 <!-- the program does not seem to generate a dot plot, even though that is implied in the help -->
63 <!--<data format="tar" name="imagesFile" label="RNALalifold images"/>-->
64 </outputs>
65 <tests>
66 <test>
67 <param name="input" value="rnalalifold_input1.clustal"/>
68 <output name="output" file="rnalalifold_result1.txt"/>
69 </test>
70 </tests>
71 <help>
72 <![CDATA[
73
74 **RNALalifold**
75
76 Calculates locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n and a base pair span 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 RNA
77
78
79 -----
80
81 **Input format**
82
83 RNALalifold requires one input file
84 - Clustal file
85
86 ------
87
88 **Outputs**
89
90 - energy of the consensus structures in the clustal file
91 - several possible postscript images bundled together in a tar file
92
93
94 ]]>
95 </help>
96 <expand macro="citations" />
97 </tool>