Mercurial > repos > rnateam > viennarna_rnaalifold

annotate rnaalifold.xml @ 0:9e1a9e069a4c draft

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 78112b796295701aabd1ee2268983222f0d27374
author rnateam
date Wed, 05 Oct 2016 16:37:11 -0400
parents
children 40b99ecd575f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
1 <tool id="viennarna_rnaalifold" name="@EXECUTABLE@" version="@VERSION@.0">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
2 <description>Calculate minimum free energy secondary structures and partition function on a multiple alignment file</description>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
3 <macros>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
4 <token name="@EXECUTABLE@">RNAalifold</token>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
5 <import>macros.xml</import>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
6 </macros>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
7 <expand macro="requirements" />
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
8 <expand macro="stdio" />
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
9 <expand macro="version_command" />
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
10 <command>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
11 <![CDATA[
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
12
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
13 RNAalifold < '$input' > '$tabularFile'
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
14 -T$model_options.temperature -d$model_options.dangling
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
15 $general_options.verbose
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
16 $general_options.color
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
17 $general_options.alignment
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
18 #if $general_options.layout_type ==0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
19 --layout-type=$general_options.layout_type
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
20 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
21 $general_options.noPS
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
22 #if str($IDs.id_prefix) <> "alignment"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
23 --id-prefix='$IDs.id_prefix'
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
24 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
25 $IDs.continuous_ids
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
26 $IDs.auto_id
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
27 #if $IDs.id_digits <> 4
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
28 --id-digits=$IDs.id_digits
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
29 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
30 #if $IDs.id_start <> 1
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
31 --id-start=$IDs.id_start
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
32 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
33 #if $constraints.maxBPspan <> -1
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
34 --maxBPspan=$constraints.maxBPspan
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
35 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
36 #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
37 --constraint='$constraints.constraintLocation.constraintsFile'
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
38 $constraints.constraintLocation.batch
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
39 $constraints.ss_cons
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
40 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
41 #if str($constraints.shapeOption.shapeSelector) == "isUsed"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
42 #if len($constraints.shapeOption.shape_files) > 0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
43 #set $sf=list()
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
44 #for $i in $constraints.shapeOption.shape_files
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
45 $sf.append(str('$i.shape'))
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
46 #end for
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
47 --shape= #echo ','.join($sf)
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
48 #if $constraints.shapeOption.m <> 1.8 or $constraints.shapeOption.b <> -0.6
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
49 #set $s="Dm"+str($constraints.shapeOption.m)+"b"+str($constraints.shapeOption.b)
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
50 --shapeMethod=$s
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
51 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
52 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
53 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
54 #if $algorithm_options.pf <> "-1"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
55 --partfunc=$algorithm_options.pf
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
56 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
57 #if $algorithm_options.mea <> 1.0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
58 --mea=$algorithm_options.mea
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
59 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
60 $algorithm_options.mis
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
61 #if $algorithm_options.stochBT_en <> 1
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
62 --stochBT_en=$algorithm_options.stochBT_en
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
63 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
64 #if $algorithm_options.pfScale <> 1.07
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
65 --pfScale=$algorithm_options.pfScale
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
66 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
67 $algorithm_options.circular
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
68 #if $algorithm_options.bppmThreshold <> 1e-6
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
69 --bppmThreshold=$algorithm_options.bppmThreshold
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
70 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
71 $algorithm_options.gquad
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
72 $algorithm_options.sci
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
73 $model_options.notetra
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
74 $model_options.nolp
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
75 $model_options.nogu
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
76 $model_options.noclosinggu
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
77 #if $model_options.cfactor <> 1.0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
78 --cfactor=$model_options.cfactor
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
79 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
80 #if $model_options.nfactor <> 1.0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
81 --nfactor=$model_options.nfactor
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
82 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
83 $model_options.endgaps
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
84 $model_options.ribosum
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
85 #if $model_options.nsp
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
86 --nsp='$model_options.nsp'
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
87 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
88 #if $model_options.betaScale <> 1.0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
89 --betaScale=$model_options.betaScale
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
90 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
91 && tar -cf '$imagesFile' *.ps
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
92 ]]>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
93 </command>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
94 <inputs>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
95 <param format="txt" name="input" type="data" label="Clustal file"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
96 <section name="algorithm_options" title="Algorithm Options">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
97 <param name="pf" type="select" label="Calculate partition function" help="Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only." argument="-p">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
98 <option value="-1" selected="true">None</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
99 <option value="0">0: Deactivates the calculation of the pair probabilities, saving about 50% in runtime</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
100 <option value="1" >1: Calculate the partition function and base pairing probability matrix</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
101 </param>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
102 <param name="mea" type="float" value="1.0" label="Gamma Value" help="Calculate an MEA (maximum expected accuracy) structure. The parameter gamma tunes the importance of correctly predicted pairs versus unpaired bases. Thus, for small values of gamma the MEA structure will contain only pairs with very high probability. where the expected accuracy is computed from the pair probabilities: each base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired base is given by the probability of not forming a pair." argumen="--MEA"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
103 <param argument="--mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="Output 'most informative sequence' instead of simple consensu"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
104 <param name="stochBT_en" type="integer" value="1" label="Number of random structures." help="Compute a certain number of random structures with a probability dependend on the partition function. Print out the energies and probabilities of the backtraced structures. " argument="--stochBT_en"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
105 <param name="pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences." argumen="--pfScale"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
106 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
107 <param name="bppmThreshold" type="float" value="1e-6" label="Threshold for base pair probabilities" help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data." argumen="--bppmThreshold"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
108 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="Take into account G Quadruplex formation (-g)"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
109 <param name="sci" type="boolean" truevalue="--sci" falsevalue="" checked="false" label="Structure conservation index"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
110 help="Compute the structure conservation index (SCI) for the MFE consensus structure of the alignment" argument="--sci"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
111 </section>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
112 <section name="general_options" title="General Options">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
113 <param name="verbose" type="boolean" truevalue="--v" falsevalue="" checked="false" label=" Be verbose" argument="--v"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
114 <param name="color" type="boolean" truevalue="--color" falsevalue="" checked="false" label="Colored secondary structure image"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
115 help="Produce a colored version of the consensus strcture plot" argument="--color"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
116 <param name="alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
117 label="Colored and annotated alignment image"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
118 help="Produce a colored and structure annotated alignment"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
119 argument="--aln"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
120 <param name="layout_type" type="select" label="Layout algorithm" argument="--layout-type">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
121 <option value="1" selected="true">Default: Naview layout</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
122 <option value="0">Simple radial layout</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
123 </param>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
124 <param name="noPS" type="boolean" truevalue="" falsevalue="--noPS" checked="true" label="Produce postscript output" help="" argument="--noPS"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
125 </section>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
126 <section name="IDs" title="Naming Conventions">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
127 <param name="continuous_ids"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
128 type="boolean" truevalue="--continuous-ids" falsevalue="" checked="false"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
129 label="Continuous alignment ID numbering"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
130 help="Use continuous alignment ID numbering when no alignment ID can be retrieved from input data."
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
131 argument="--continuous-ids"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
132 <param name="auto_id"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
133 type="boolean" truevalue="--auto-id" falsevalue="" checked="false"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
134 label="Automatically generate an ID for each alignment."
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
135 help="If this flag is active, RNAalifold ignores any IDs retrieved from the input and automatically generates an ID for each alignment."
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
136 argument="--auto-id"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
137 <param name="id_prefix"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
138 type="text" value="alignment"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
139 label="Prefix for automatically generated IDs (as used in output file names)"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
140 help="If this parameter is set, each alignment will be prefixed with the provided string. Hence, the output files will obey the following naming scheme: 'prefix_xxxx_ss.ps' (secondary structure plot), 'prefix_xxxx_dp.ps' (dot−plot), 'prefix_xxxx_aln.ps' (annotated alignment), etc. where xxxx is the alignment number beginning with the second alignment in the input. Use this setting in conjunction with the −−continuous−ids flag to assign IDs beginning with the first input alignment."
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
141 argument="--id-prefix"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
142 <param name="id_digits"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
143 type="integer" value="4" min="1" max="18"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
144 label="The number of digits of the counter in automatically generated alignment IDs"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
145 help="When alignments IDs are automatically generated, they receive an increasing number, starting with 1. This number will always be left−padded by leading zeros, such that the number takes up a certain width. Using this parameter, the width can be specified to the users need. We allow numbers in the range [1:18]."
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
146 argument="--id-digits"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
147 <param name="id_start"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
148 type="integer" value="1" min="0"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
149 label="First number in automatically generated alignment IDs"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
150 help="When alignment IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous alignment IDs, i.e. it activates the −−continuous−ids flag.."
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
151 argument="--id-start"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
152 </section>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
153 <section name="constraints" title="Structure constraints">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
154 <param name="maxBPspan" type="integer" value="-1" label="Set the maximum base pair span" help="" argument="--maxBPspan"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
155 <conditional name="constraintLocation">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
156 <param name="constraintSelector" type="select" label="Constraints" argument="--constraint">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
157 <!-- <option value="fromInput">The constraints are included in the input file</option> -->
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
158 <option value="fromFile">The constraints are in a seperate file</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
159 <option value="none" selected="true">Don't use constraints</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
160 </param>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
161 <!-- <when value="fromInput"></when> -->
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
162 <when value="none"></when>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
163 <when value="fromFile">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
164 <param name="constraintsFile" type="data" format="*" label="Constraints file"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
165 <param name="batch" type="boolean" checked="false" truevalue="--batch" falsevalue=""
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
166 label="Use constraints for all alignment records"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
167 help="Usually, constraints provided from input file are only applied to a single sequence alignment. Therefore, RNAalifold will stop its computation and quit after the first input alignment was processed. Using this switch, RNAalifold processes all sequence alignments in the input and applies the same provided constraints to each of them."
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
168 argument="--batch"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
169 <param name="ss_cons" type="boolean" checked="false" truevalue="--SS_cons" falsevalue=""
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
170 label="Use consensus structures from Stockholm file (#=GF SS_cons) as constraint"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
171 help="Stockholm formatted alignment files have the possibility to store a secondary structure string in one of if ('#=GC') column annotation meta tags. The corresponding tag name is usually 'SS_cons', a consensus secondary structure. Activating this flag allows one to use this consensus secondary structure from the input file as structure constraint. Note: Activating this flag implies −−constraint."
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
172 argument="--SS_cons"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
173 </when>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
174 </conditional>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
175 <conditional name="shapeOption">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
176 <param name="shapeSelector" type="select" label="Shape reactivity data">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
177 <option value="isUsed">Use shape reactivity data</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
178 <option value="notUsed" selected="true">Don't use shape reactivity data</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
179 </param>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
180 <when value ="isUsed">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
181 <repeat name="shape_files" title="Shape File" default="0" argument="--shape">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
182 <param type="data" name="shape" format="shape,*" label="Shape file"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
183 </repeat>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
184 <param name="m" type="float" value="1.8" label="Slope m" />
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
185 <param name="b" type="float" value="-0.6" label="Intercept b" help="Currently, the only data conversion method available is that of to Deigan et al 2009. This method is the default. The slope 'm' and the intercept 'b' can be set to a non−default value if necessary. Otherwise m=1.8 and b=−0.6 as stated in the paper mentioned before."/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
186 </when>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
187 <when value="notUsed">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
188 </when>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
189 </conditional>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
190 </section>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
191 <section name="model_options" title="Model Options" expanded="true">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
192 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
193 <param name="dangling" type="select" label="How to treat dangling end energies" help="-d">
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
194 <option value="0">0: ignore dangling ends</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
195 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
196 </param>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
197 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
198 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
199 <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"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
200 <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)"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
201 <param name="cfactor" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
202 <param name="nfactor" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
203 <param name="endgaps" type="boolean" truevalue="--endgaps" falsevalue="" checked="false" label="Score pairs with endgaps same as gap-gap pairs" help="--endgaps"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
204 <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
205 <param name="nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs." help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy." argument="--nsp"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
206 <param name="betaScale" type="float" value="1.0" label="Scaling of Boltzman factors"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
207 help=" The argument provided with this option enables to scale the thermodynamic temperature used in the Boltzmann factors independently from the temperature used to scale the individual energy contributions of the loop types."
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
208 argument="--betaScale"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
209 </section>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
210 </inputs>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
211 <outputs>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
212 <data format="txt" name="tabularFile"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
213 <data format="tar" name="imagesFile"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
214 </outputs>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
215 <tests>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
216 <test>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
217 <param name="input" value="rnaalifold_input1.clustal"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
218 <output name="output" file="rnaalifold_result1.txt"/>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
219 </test>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
220 </tests>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
221 <help>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
222 <![CDATA[
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
223 **RNAalifold**
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
224
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
225 -----
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
226
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
227 **Input format**
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
228
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
229 RNAalifold requires one input file
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
230 - Clustal file
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
231
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
232 ------
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
233
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
234 **Outputs**
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
235
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
236 - energy of the consensus structures in the clustal file
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
237 - several possible postscript images bundled together in a tar file
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
238
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
239
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
240 ]]>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
241 </help>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
242 <expand macro="citations" />
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
rnateam
parents:
diff changeset
243 </tool>