Mercurial > repos > bgruening > dotknot

annotate dotknot.xml @ 1:12fd4ac417fe 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/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
author bgruening
date Thu, 17 Sep 2015 16:51:55 -0400
parents 7d7194e4a205
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
1 <tool id="dotknot" name="DotKnot" version="1.3.1">
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
2 <description>pseudoknot prediction in a given RNA sequence</description>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
3 <requirements>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
4 <requirement type="package" version="1.8.5">vienna_rna</requirement>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
5 <requirement type="package" version="1.3.1">dotknot</requirement>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
6 </requirements>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
7 <stdio>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
8 <exit_code range="1:" />
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
9 <exit_code range=":-1" />
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
10 <regex match="Error:" />
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
11 <regex match="Exception:" />
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
12 </stdio>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
13 <version_command>dotknot version 1.3.1</version_command>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
14 <command><![CDATA[
1
12fd4ac417fe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
bgruening
parents: 0
diff changeset
15 cp \$DOTKNOT_ROOT_PATH/* ./ -R &&
0
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
16 dotknot.py
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
17 $input
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
18 $k
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
19 $l
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
20 $g
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
21 > ./output.txt
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
22 #if $g:
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
23 &&
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
24 mv ./*.ct ./globalstructure.ct
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
25 #end if
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
26 ]]></command>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
27 <inputs>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
28 <param name="input" type="data" format="fasta" label="Upload your FASTA file with RNA sequences:"
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
29 help="The FASTA file must contain a comment line starting with > followed by the sequence.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
30 It can also contain several consecutive sequences and DotKnot will be executed for each sequence in the file."/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
31
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
32 <param argument="-k" type="boolean" checked="false"
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
33 truevalue="-k" falsevalue=""
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
34 label="Include kissing hairpins?"
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
35 help="Kissing hairpins are complex and biologically relevant types of pseudoknots.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
36 Inclusion of kissing hairpins will lead to increased run time,
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
37 yet produce more meaningful results."/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
38
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
39 <param argument="-l" type="boolean" checked="false"
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
40 truevalue="-l" falsevalue=""
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
41 label="Include near-optimal local pseudoknots?"
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
42 help="Shows top five near-optimal local pseudoknots in terms of two criteria:
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
43 estimated free energy to length ratio and lowest estimated free energy.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
44 This can help to identify promising pseudoknot foldings and may
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
45 compensate for the limitations of the energy parameters."/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
46
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
47 <param argument="-g" type="boolean" checked="false"
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
48 truevalue="-g" falsevalue=""
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
49 label="Include global structure?"
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
50 help="Shows predicted global structure in addition to predicted pseudoknots."/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
51
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
52 </inputs>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
53 <outputs>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
54 <data name="output" format="txt" from_work_dir="./output.txt"
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
55 label="${tool.name} on ${on_string} (output file)">
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
56 </data>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
57 <data name="outfile_globalstructure" format="txt" from_work_dir="./globalstructure.ct"
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
58 label="${tool.name} on ${on_string} (output global structure)">
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
59 <filter>g == True</filter>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
60 </data>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
61 </outputs>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
62 <tests>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
63 <test>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
64 <param name="input" value="TMV.fasta" ftype="fasta"/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
65 <param name="k" value=""/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
66 <param name="l" value=""/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
67 <param name="g" value=""/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
68 <output name="output" file="test1_output.txt" ftype="txt"/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
69 </test>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
70 <test>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
71 <param name="input" value="HCoV229E_short_KISSINGHAIRPINS.fasta" ftype="fasta"/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
72 <param name="k" value="-k"/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
73 <param name="l" value="-l"/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
74 <param name="g" value="-g"/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
75 <output name="output" file="test2_output.txt" ftype="txt"/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
76 <output name="outfile_globalstructure" file="test2_output2.ct" ftype="txt"/>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
77 </test>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
78 </tests>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
79 <help><![CDATA[
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
80
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
81 **WHAT IT DOES**
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
82
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
83 DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
84
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
85 DotKnot extracts stem regions from the secondary structure probability dot plot calculated by RNAfold. Recursive H-type pseudoknots and intramolecular kissing hairpins are constructed and their presence in the sequence is verified. The detected pseudoknots can then be further analysed using bioinformatics or laboratory techniques.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
86
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
87 -----
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
88
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
89 **INPUT**
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
90
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
91 The FASTA file must contain a comment line starting with > followed by the sequence. It can also
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
92 contain several consecutive sequences and DotKnot will be executed for each sequence in the file.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
93
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
94 Please ensure that only bases A,C,G,U,T (a,c,g,u,t) are used.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
95
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
96 *Example*::
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
97
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
98 > Arc-Ful-SRP short
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
99 GGGGGGUUCGGCGUCCCCUGUAACCCGAAACCGCCGAUACGCGGG
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
100 > MMTV
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
101 AAAAAACUUGUAAAGGGGCAGUCCCCUAGCCCCGCUCAAAAGGGGGAUG
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
102
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
103 -----
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
104
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
105 **OPTIONAL ARGUMENTS**
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
106
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
107 *Kissing hairpins*::
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
108 Kissing hairpins are complex and biologically relevant types of pseudoknots.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
109 Inclusion of kissing hairpins will lead to increased run time, yet produce more meaningful
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
110 results.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
111
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
112 *local pseudoknots*::
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
113 Shows top five near-optimal local pseudoknots in terms of two criteria: estimated free energy
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
114 to length ratio and lowest estimated free energy. This can help to identify promising pseudoknot
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
115 foldings and may compensate for the limitations of the energy parameters.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
116 *global structure*::
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
117 Shows predicted global structure in addition to predicted pseudoknots
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
118
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
119 -----
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
120
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
121 **OUTPUT**
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
122
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
123 Each pseudoknot is displayed in dot-bracket notation. Unpaired bases are indicated by dots. Base
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
124 pairs are written as bracket pairs. The first stem of a pseudoknot is indicated by round brackets , i.e. ( and ). The second stem of a pseudoknot is indicated by square brackets, i.e. [ and ].
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
125
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
126 We also give the start and end positions of the pseudoknot with respect to the input sequence. If the global structure option is chosen (-g:), a CT file will be created which contains the global
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
127 structure. The file name will start with the identifier given in the FASTA file.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
128
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
129 -----
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
130
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
131 **dotknot** is a Free and Open Source Software, see more details and background information on the dotknot dotknot_ Website.
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
132
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
133 .. _dotknot: http://dotknot.csse.uwa.edu.au/
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
134
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
135 ]]></help>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
136 <citations>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
137 <citation type="doi">10.1093/nar/gkq021</citation>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
138 <citation type="doi">10.1261/rna.2394511</citation>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
139 </citations>
7d7194e4a205 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 6def0606119579a9adbc09c171b87a2bcac7236d-dirty
bgruening
parents:
diff changeset
140 </tool>