Mercurial > repos > rnateam > viennarna_kinwalker
annotate kinwalker.xml @ 2:aad9e6557d00 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty
author | rnateam |
---|---|
date | Thu, 28 Sep 2017 16:24:16 -0400 |
parents | b13a2b5a811a |
children |
rev | line source |
---|---|
0
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
1 <tool id="viennarna_kinwalker" name="@EXECUTABLE@" version="@VERSION@.0"> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
2 <description>cotranscriptional folding of RNAs</description> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
3 <macros> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
4 <token name="@EXECUTABLE@">kinwalker</token> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
5 <import>macros.xml</import> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
6 </macros> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
7 <expand macro="requirements" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
8 <expand macro="stdio" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
9 <expand macro="version_command" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
10 <command> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
11 <![CDATA[ |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
12 head -n 1 '$input_sequence' | head -c -1 -q > seq.ident |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
13 && |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
14 sed '1d' '$input_sequence' > input.seq |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
15 && |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
16 kinwalker |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
17 $init_structure |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
18 $interrupt |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
19 ##$printfront |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
20 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
21 --barrier_heuristic $barrier_heuristic.used |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
22 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
23 #if $barrier_heuristic.used == "M" |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
24 --grouping $barrier_heuristic.grouping |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
25 --lookahead $barrier_heuristic.lookahead |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
26 #else if $barrier_heuristic.used == "B" |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
27 --maxkeep $barrier_heuristic.maxkeep |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
28 #end if |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
29 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
30 --dangle $dangle |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
31 --noLonelyPairs $noLonelyPairs |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
32 --transcribed $transcribed |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
33 --transcription_rate $transcription_rate |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
34 --windowsize $windowsize |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
35 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
36 < input.seq |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
37 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
38 > blah |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
39 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
40 && |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
41 sed -n '2s/[\.\(\)]\+\s\+\(.\+\)$/ mfe: \1/p' blah > energy |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
42 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
43 && |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
44 cat seq.ident energy > '$mfe_struct' |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
45 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
46 && |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
47 sed -e '2s/^\([\.\(\)]\+\).*$/\1/' -ne '1,2p' blah >> '$mfe_struct' |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
48 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
49 && |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
50 sed -e 's/[ \t]*$//' -ne '/TRAJ/,/Kinwal/ {/TRAJ/n;/Kinwal/!{s/\s/\t/gp}}' blah > '$trajectory' |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
51 ]]> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
52 </command> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
53 <inputs> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
54 <param name="input_sequence" format="fasta" type="data" label="Input sequence" help="A single sequence in FASTA format"/> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
55 <param name="init_structure" type="boolean" truevalue="--init_structure" falsevalue="" checked="false" label="Start with a structure other than the open chain" help="(--init_structure)"/> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
56 <param name="interrupt" type="boolean" truevalue="--interrupt" falsevalue="" checked="false" label="Allow interrupted folding trajectories when the barrier is exceeded" help="(--interrupt)"/> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
57 <!-- need to implement with dataset collections <param name="printfront" type="boolean" truevalue="!doublehypen!printfront" falsevalue="" checked="true" label="Creates PS plots of front progression" help="(!doublehypen!printfront)"/> --> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
58 <conditional name="barrier_heuristic"> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
59 <param name="used" type="select" label="Barrier Heuristic" help="(--barrier_heuristic)"> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
60 <option value="M" selected="true">Morgan-Higgs</option> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
61 <option value="S">Limit small stacks</option> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
62 <option value="B">Barriers</option> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
63 <option value="A">All</option> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
64 </param> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
65 <when value="M"> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
66 <param name="grouping" type="select" label="How to treat conflict groups" help="(--grouping)"> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
67 <option value="standard" selected="true">Standard</option> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
68 <option value="regroup">Re-group</option> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
69 </param> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
70 <param name="lookahead" type="integer" value="1" label="Number of basepairs that MorganHiggs forms its subpaths from" help="(--lookahead)"/> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
71 </when> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
72 <when value="S" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
73 <when value="B"> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
74 <param name="maxkeep" type="integer" value="1" label="Breadth of breadth first search" help="(--maxkeep)"/> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
75 </when> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
76 <when value="A" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
77 </conditional> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
78 <param name="dangle" type="select" label="Dangle value as in VienneRNA package" help="(--dangle)"> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
79 <option value="0" selected="true">0</option> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
80 <option value="1">1</option> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
81 <option value="2">2</option> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
82 </param> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
83 <param name="noLonelyPairs" type="integer" value="2" label="Value of noLonelyPairs as in ViennaRNA" help="(--noLonelyPairs)"/> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
84 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
85 <param name="transcribed" type="integer" value="1" label="Number of bases initially transcribed" help="0 means all is transcribed (--transcribed)"/> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
86 <param name="transcription_rate" type="float" value="200" label="Number of bases transcribed per second" help="(--transcription_rate)"/> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
87 <param name="windowsize" type="integer" value="0" label="Max size of substructures considered for folding events during transcription" help="0= all are considered. (--windowsize)"/> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
88 </inputs> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
89 <outputs> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
90 <data format="fasta" name="mfe_struct" label="MFE structure from ${tool.name} on ${on_string}" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
91 <data format="tabular" name="trajectory" label="Trajectory of ${tool.name} on ${on_string}" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
92 </outputs> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
93 <tests> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
94 <test> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
95 <param name="input_sequence" value="test_sequence_input.fasta" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
96 <param name="init_structure" value="" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
97 <param name="interrupt" value="" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
98 <param name="used" value="M" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
99 <param name="grouping" value="standard" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
100 <param name="lookahead" value="1" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
101 <param name="dangle" value="0" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
102 <param name="noLonelyPairs" value="2" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
103 <param name="transcribed" value="1" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
104 <param name="transcription_rate" value="200" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
105 <param name="windowsize" value="0" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
106 <output name="mfe_struct" file="mfe_struct_result.fasta" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
107 <output name="trajectory" file="trajectory_result.tabular" /> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
108 </test> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
109 </tests> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
110 <help> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
111 <![CDATA[ |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
112 **What it does** |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
113 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
114 Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. In each transcription event one base from the RNA sequence is appended to the already transcribed and (partially) folded subsequence. |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
115 Kinwalker executes transcription events at regular time intervals. In each folding event a subsequence of the already transcribed RNA sequence is selected and a new structure is formed by combining base pairs from the current structure with base pairs from the mfE structure of that subsequence. |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
116 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
117 This is done in such a way that the new structure includes base pairs from both structures in an energetically favorable manner. Kinwalker estimates the waiting times for individual folding events depending on the height of the energy barrier between the current structure and the new structure into which the molecule is folded. Folding events between structures can only occur, if the energy barrier between them is less than the maximum allowed energy barrier. |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
118 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
119 As folding paths can only be calculated exhaustively for short sequences (n>100), heuristic approaches have to be employed which explicitly construct a (re)folding path between the two structures. The saddle height is then estimated as the highest point along the path. The best known algorithm for approximating saddle heights between RNA conformations is the Morgan-Higgs heuristic, which tries to find a folding path from an origin secondary structure to a target secondary structure where the maximum height along the path is minimal. The heuristic models state transitions at base pair resolution. |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
120 ]]> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
121 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
122 **Input** |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
123 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
124 RNA sequence in FASTA format |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
125 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
126 **Output** |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
127 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
128 RNA folding trajectory |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
129 |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
130 </help> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
131 <citations> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
132 <citation type="doi">10.1016/j.jmb.2008.02.064</citation> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
133 </citations> |
b13a2b5a811a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
parents:
diff
changeset
|
134 </tool> |