Mercurial > repos > rnateam > viennarna_rnapkplex

annotate rnapkplex.xml @ 6:339ad356faa1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 08:32:47 -0500
parents 289f7e5b3d51
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
1 <tool id="viennarna_rnapkplex" name="@EXECUTABLE@" version="@VERSION@.0">
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
2 <description> predicts RNA secondary structures including pseudoknots</description>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
3
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
4 <macros>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
5 <token name="@EXECUTABLE@">RNAPKplex</token>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
6 <import>macros.xml</import>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
7 </macros>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
8 <expand macro="requirements" />
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
9 <expand macro="stdio" />
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
10 <expand macro="version_command" />
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
11 <command>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
12 <![CDATA[
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
13 RNAPKplex < '$input' > '$output'
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
14 -T$temperature
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
15 --energyCutoff=$energycutoff
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
16 #if $varExists('$advancedOptions.nolp')
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
17 --cutoff=$advancedOptions.cutoff
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
18 --subopts=$advancedOptions.suboptimal
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
19 $advancedOptions.verbose
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
20 $advancedOptions.noconversion
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
21 $advancedOptions.nolp
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
22 $advancedOptions.nogu
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
23 $advancedOptions.noclosinggu
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
24 $advancedOptions.notetra
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
25 #end if
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
26 ]]>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
27 </command>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
28
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
29 <inputs>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
30 <param format="fasta" name="input" type="data" label="Fasta file"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
31 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
32 <param name="energycutoff" type="float" value="-8.1" label="Pseudoknots cutoff. Pseudoknots with smaller energy gains are rejected." help="--energyCutoff"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
33 <conditional name="advancedOptions">
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
34 <param name="advancedSelector" type="select" label="advanced options">
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
35 <option value="basic">basic Options</option>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
36 <option value="advanced">advanced Options</option>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
37 </param>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
38 <when value="advanced">
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
39 <param name="suboptimal" type="float" value="0.0" label="Print suboptimal pseudoknots" help="--subopts"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
40 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose mode, more output" help="--verbose"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
41 <param name="cutoff" type="float" value="0.01" label="cutoff probability for the reporting of the base pairs in the dot plot" help="--cutoff"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
42 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
43 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
44 <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"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
45 <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)"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
46 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
47 </when>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
48 <when value="basic">
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
49 </when>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
50 </conditional>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
51 </inputs>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
52 <outputs>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
53 <data format="txt" name="output"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
54 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
55 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.ps" ext="eps" />
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
56 </collection>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
57 </outputs>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
58 <tests>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
59 <test>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
60 <param name="input" value="rnapkplex_input1.fa"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
61 <output name="out_file" file="rnapkplex_result1.txt"/>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
62 </test>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
63 </tests>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
64 <help>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
65 <![CDATA[
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
66
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
67 **RNAPKplex**
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
68
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
69 Computes RNA secondary structures by first making two sequence intervals accessible and unpaired using the algorithm of RNAplfold and then calculating the energy of the interaction of those two intervals. The algorithm uses O(n^2*w^4) CPU time and O(n*w^2) memory space. The algorithm furthermore always considers dangle=2 model.
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
70
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
71 It also produces a PostScript file with a plot of the pseudoknot-free secondary structure graph, in which the bases forming the pseuodknot are marked red.
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
72
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
73 For each structure in the Fasta input, a PostScript file is produced for the structure graph.
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
74
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
75 -----
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
76
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
77 **Input format**
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
78
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
79 RNAPKplex requires one input file
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
80
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
81 - fasta file
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
82
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
83 The input format is similar to fasta except that even long sequences may not be interrupted by line breaks, and the header lines are optional.
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
84
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
85 ------
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
86
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
87 **Outputs**
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
88
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
89 - secondary structure in dot-bracket format
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
90 - Images of the calculated structures
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
91
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
92 ]]>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
93 </help>
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
94 <expand macro="citations" />
289f7e5b3d51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff changeset
95 </tool>