Mercurial > repos > rnateam > vienna_rna
comparison rnacofold.xml @ 0:78d673470d45 draft
Imported from capsule None
author | rnateam |
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date | Wed, 04 Feb 2015 12:05:27 -0500 |
parents | |
children | 5e58cbf27a05 |
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-1:000000000000 | 0:78d673470d45 |
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1 <tool id="rnacofold" name="RNAcofold" version="2.1.6.0"> | |
2 <description>Calculate secondary structures of two RNAs with dimerization</description> | |
3 <expand macro="requirements" /> | |
4 <expand macro="version_command" /> | |
5 <expand macro="stdio" /> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">RNAcofold</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <command> | |
11 <![CDATA[ | |
12 RNAcofold < $input > $tabularFile | |
13 -T$temperature -d$dangling | |
14 $pf | |
15 $allpf | |
16 #if $varExists('$advancedOptions.noconversion') | |
17 $advancedOptions.constraint | |
18 $advancedOptions.noconversion | |
19 $advancedOptions.gquad | |
20 $advancedOptions.nolp | |
21 $advancedOptions.nogu | |
22 $advancedOptions.noclosinggu | |
23 $advancedOptions.notetra | |
24 #end if | |
25 ]]> | |
26 </command> | |
27 <inputs> | |
28 <param format="fasta" name="input" type="data" label="Fasta file"/> | |
29 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="-T"/> | |
30 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d"> | |
31 <option value="0">0: ignore dangling ends</option> | |
32 <option value="1">1: unpaired bases participate in one dangling end only</option> | |
33 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option> | |
34 <option value="3">3: allow coaxial stacking</option> | |
35 </param> | |
36 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/> | |
37 <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers" help="--all_pf"/> | |
38 <conditional name="advancedOptions"> | |
39 <param name="advancedSelector" type="select" label="advanced options"> | |
40 <option value="basic">basic Options</option> | |
41 <option value="advanced">advanced Options</option> | |
42 </param> | |
43 <when value="advanced"> | |
44 <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structure subject to constraints" help="--constraint"/> | |
45 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion T->U" help="--noconv"/> | |
46 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/> | |
47 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/> | |
48 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> | |
49 <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/> | |
50 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/> | |
51 </when> | |
52 </conditional> | |
53 </inputs> | |
54 <outputs> | |
55 <data format="txt" name="tabularFile"/> | |
56 <collection name="sequence_outputs" type="list" label="rna_eps outputs"> | |
57 <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" /> | |
58 </collection> | |
59 <collection name="matrix_outputs" type="list" label="rna_eps outputs"> | |
60 <filter>pf is True</filter> | |
61 <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> | |
62 </collection> | |
63 </outputs> | |
64 <tests> | |
65 </tests> | |
66 <help> | |
67 <![CDATA[ | |
68 **RNAcofold** | |
69 | |
70 | |
71 ----- | |
72 | |
73 **Input format** | |
74 | |
75 RNAcofold requires one input file: | |
76 | |
77 - Fasta file | |
78 | |
79 Two different RNA sequences can be specified concatenated with the '&' character. The folding of the two sequences with each other will be calculated. | |
80 | |
81 | |
82 ------ | |
83 | |
84 **Outputs** | |
85 | |
86 - Energies of the RNA sequences and the dimers | |
87 - Structure images | |
88 - Dot Plot Matrix images (if --partfunc is used) | |
89 | |
90 ]]> | |
91 </help> | |
92 <expand macro="requirements" /> | |
93 </tool> |