annotate antarna.xml @ 2:cfe9e6771518 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
author rnateam
date Wed, 13 May 2015 11:17:08 -0400
parents ebc371f3c6b5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
1 <tool id="antarna" name="antaRNA" version="1.1">
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
2 <description>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
3 Ant Colony Optimized RNA Sequence Design
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
4 </description>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
5 <requirements>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
6 <requirement type="package" version="2.2.12">pkiss</requirement>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
7 <requirement type="package" version="3.2.5">rnashapes</requirement>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
8 <requirement type="package" version="1.7.1">numpy</requirement>
1
ebc371f3c6b5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents: 0
diff changeset
9 <requirement type="package" version="2.1">vienna_rna</requirement>
0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
10 </requirements>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
11 <stdio>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
12 <exit_code level="fatal" range="1:"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
13 </stdio>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
14 <version_command>python antaRNA.py --version</version_command>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
15 <command interpreter="python"><![CDATA[antaRNA.py
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
16 #if $Cstr and $Cstr is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
17 -Cstr "$Cstr"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
18 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
19
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
20 #if $tGC and $tGC is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
21 -tGC $tGC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
22 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
23
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
24 #if $n and $n is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
25 -n $n
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
26 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
27 $GU
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
28
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
29 #if $s and $s is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
30 -s $s
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
31 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
32
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
33 #if $ip and $ip is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
34 -ip $ip
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
35 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
36
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
37 #if $r and $r is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
38 -r $r
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
39 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
40
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
41 #if $CC and $CC is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
42 -CC $CC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
43 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
44
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
45 #if $aTC and $aTC is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
46 -aTC $aTC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
47 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
48 $p
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
49 $pkPar
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
50
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
51 #if $strategy and $strategy is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
52 --strategy $strategy
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
53 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
54
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
55 #if $tGCmax and $tGCmax is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
56 -tGCmax $tGCmax
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
57 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
58
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
59 #if $tGCvar and $tGCvar is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
60 -tGCvar $tGCvar
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
61 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
62
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
63 #if $t and $t is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
64 -t $t
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
65 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
66
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
67 #if $P and $P is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
68 -P $P
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
69 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
70
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
71 #if $of and $of is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
72 -of $of
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
73 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
74
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
75 #if $Cseq and $Cseq is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
76 -Cseq $Cseq
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
77 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
78
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
79 #if $l and $l is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
80 -l $l
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
81 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
82
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
83 #if $name and $name is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
84 --name $name
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
85 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
86
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
87 #if $a and $a is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
88 -a $a
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
89 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
90
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
91 #if $b and $b is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
92 -b $b
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
93 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
94
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
95 #if $er and $er is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
96 -er $er
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
97 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
98
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
99 #if $Cstrw and $Cstrw is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
100 -Cstrw $Cstrw
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
101 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
102
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
103 #if $Cgcw and $Cgcw is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
104 -Cgcw $Cgcw
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
105 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
106
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
107 #if $Cseqw and $Cseqw is not None:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
108 -Cseqw $Cseqw
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
109 #end if
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
110 $ov
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
111 $v
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
112 > $default]]></command>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
113 <inputs>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
114 <param label="Structure constraint using RNA dotbracket notation with fuzzy block constraint. (-Cstr)" name="Cstr" type="text"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
115 <param label="Objective target GC content in [0,1]. (-tGC)" name="tGC" type="float" value="0"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
116 <param label="Number of sequences which shall be produced. (-n)" name="n" type="integer" value="0"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
117 <param checked="false" label="Allowing GU base pairs. (-GU)" name="GU" type="boolean" truevalue="-GU" falsevalue=""/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
118 <param default="none" label="Provides a seed value for the used pseudo random number generator. (-s)" name="s" type="text"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
119 <param default="s" label="Select the improving method. h=hierarchical, s=score_based. (-ip)" name="ip" type="text"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
120 <param label="Amount of maximal terrain resets, until the best solution is retuned as solution. (-r)" name="r" type="integer" value="5"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
121 <param label="Delimits the convergence count criterion for a reset. (-CC)" name="CC" type="integer" value="130"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
122 <param label="Delimits the amount of internal ants for termination convergence criterion for a reset. (-aTC)" name="aTC" type="integer" value="50"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
123 <param checked="false" label="Switch to pseudoknot based prediction using pKiss. Check the pseudoknot parameter usage!!! (-p)" name="p" type="boolean" truevalue="-p" falsevalue=""/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
124 <param checked="false" label="Enable optimized parameters for the usage of pseudo knots (Further parameter input ignored). (-pkPar)" name="pkPar" type="boolean" truevalue="-pkPar" falsevalue=""/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
125 <param default="A" label="Defining the pKiss folding strategy. (--strategy)" name="strategy" type="text"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
126 <param label="Provides a maximum tGC value [0,1] for the case of uniform distribution sampling. The regular tGC value serves as minimum value. (-tGCmax)" name="tGCmax" type="float" value="-1.0"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
127 <param label="Provides a tGC variance (sigma square) for the case of normal distribution sampling. The regular tGC value serves as expectation value (mu). (-tGCvar)" name="tGCvar" type="float" value="-1.0"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
128 <param label="Provides a temperature for the folding algorithms. (-t)" name="t" type="float" value="37.0"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
129 <param default="" label="Changes the energy parameterfile of RNAfold. If using this explicitly, please provide a suitable energy file delivered by RNAfold. (-P)" name="P" type="text"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
130 <param default="STDOUT" label="Provide a path and an output file, e.g. &quot;/path/to/the/target_file&quot;. (-of)" name="of" type="text"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
131 <param default="" label="Sequence constraint using RNA nucleotide alphabet {A,C,G,U} and wild-card &quot;N&quot;. (-Cseq)" name="Cseq" type="text"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
132 <param label="Sets the level of allowed influence of sequence constraint on the structure constraint [0:no influence; 3:extensive influence]. (-l)" name="l" type="integer" value="1"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
133 <param default="antaRNA_" label="Defines a name which is used in the sequence output. (--name)" name="name" type="text"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
134 <param label="Sets alpha, probability weight for terrain path influence. [0,1] (-a)" name="a" type="float" value="1.0"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
135 <param label="Sets beta, probability weight for terrain pheromone influence. [0,1] (-b)" name="b" type="float" value="1.0"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
136 <param label="Pheromone evaporation rate. (-er)" name="er" type="float" value="0.2"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
137 <param label="Structure constraint quality weighting factor. [0,1] (-Cstrw)" name="Cstrw" type="float" value="0.5"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
138 <param label="GC content constraint quality weighting factor. [0,1] (-Cgcw)" name="Cgcw" type="float" value="5.0"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
139 <param label="Sequence constraint quality weighting factor. [0,1] (-Cseqw)" name="Cseqw" type="float" value="1.0"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
140 <param checked="false" label="Displayes intermediate output. (-v)" name="v" type="boolean" truevalue="-v" falsevalue=""/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
141 <param checked="false" label="Prints additional output to the headers of the produced sequences. (-ov)" name="ov" type="boolean" truevalue="-ov" falsevalue=""/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
142 </inputs>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
143 <outputs>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
144 <data format="fasta" hidden="false" name="default">
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
145 <change_format>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
146 <when input="v" value="-v" format="txt" />
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
147 <when input="ov" value="-ov" format="txt" />
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
148 </change_format>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
149 </data>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
150 </outputs>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
151 <tests>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
152 <test>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
153 <param name="Cstr" value="((..(..((...)))..))" />
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
154 <param name="tGC" value="0.5" />
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
155 <param name="n" value="1" />
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
156 <output name="default">
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
157 <assert_contents>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
158 <has_text_matching expression="[ACGU]{19}"/>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
159 </assert_contents>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
160 </output>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
161 </test>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
162 </tests>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
163 <help><![CDATA[
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
164 .
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
165
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
166 ===========================
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
167 antaRNA - ant assembled RNA
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
168 ===========================
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
169
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
170 - antaRNA uses the VIENNNA RNA Package
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
171 - specifically it uses RNAfold and RNAdistance to calculate energies of and distances between secondary structures (version 2.1.x)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
172 - for the parametrization of antaRNA the version 2.1.3 of the ViennaRNA package was used
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
173
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
174
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
175 - For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
176
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
177 Example parameters:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
178 - --Cstr "...(((...)))..." --tGC 0.5 -n 2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
179 - --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
180 - --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
181
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
182
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
183 ]]></help>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
184 <citations>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
185 </citations>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
186 </tool>
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
parents:
diff changeset
187