annotate locarna_pairwise.xml @ 0:b4310d79bbfb draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
author bgruening
date Wed, 28 Dec 2016 18:48:14 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.0">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
2 <description>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
3 Pairwise Simultaneous Alignment and Folding of RNAs
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
4 </description>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
5
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
6 <macros>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
7 <import>macros.xml</import>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
8 </macros>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
9
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
10 <expand macro="requirements" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
11
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
12 <expand macro="stdio" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
13
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
14 <expand macro="version" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
15
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
16 <command><![CDATA[
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
17 #if str($alignment_mode.alignment_mode_selector) == "sparse"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
18 sparse
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
19 #else
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
20 locarna
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
21 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
22
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
23 '$inputA'
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
24 '$inputB'
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
25
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
26 --width 60
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
27
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
28 ## -------------------- alignment mode and specific options
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
29
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
31 #if str($alignment_mode.free_endgaps) != "----"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
32 --free-endgaps $alignment_mode.free_endgaps
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
33 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
34 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
35 --sequ-local on
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
36 #else if str($alignment_mode.alignment_mode_selector) == "structure_local_locarna"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
37 --struct-local on
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
38 #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
39 --sequ-local on
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
40 --struct-local on
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
41 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
42
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
43 ## -------------------- scoring parameters
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
44
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
45 --indel $Scoring.indel
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
46 --indel-opening $Scoring.indel_opening
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
47 --struct-weight $Scoring.struct_weight
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
48 --tau $Scoring.tau
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
49
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
50 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
51 --match $Scoring.sequence_score.match
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
52 --mismatch $Scoring.sequence_score.mismatch
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
53 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
54 --use-ribosum true
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
55 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
56 --ribofit true
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
57 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
58
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
59 ## -------------------- folding parameters
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
60
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
61 #if float($Folding.rnafold_temperature) != 37.0
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
62 --rnafold-temperature $Folding.rnafold_temperature
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
63 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
64
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
65 $Folding.alifold_consensus_dp
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
66 --consensus-structure $Folding.consensus_structure
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
67
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
68 ## -------------------- heuristic parameters
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
69
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
70 -p $Heuristics.min_prob
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
71 --max-diff-am $Heuristics.max_diff_am
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
72 --max-diff $Heuristics.max_diff
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
73 --max-diff-at-am $Heuristics.max_diff_at_am
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
74
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
75 #if float($Heuristics.max_bps_length_ratio) != 0.0
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
76 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
77 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
78
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
79 ## -------------------- other parameters
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
80
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
81 $Constraint.lonely_pairs
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
82
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
83 #if $Constraint.maxBPspan != -1
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
84 --maxBPspan $Constraint.maxBPspan
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
85 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
86
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
87 $Constraint.ignore_constraints
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
88
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
89 ## -------------------- output
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
90
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
91 #if 'stockholm' in str($outputs).split(",")
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
92 --stockholm '$stockholm'
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
93 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
94 #if 'clustal' in str($outputs).split(",")
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
95 --clustal '$clustal'
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
96 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
97 #if 'clustal_strict' in str($outputs).split(",") and (not 'clustal' in str($outputs).split(","))
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
98 --clustal '$clustal_strict'
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
99 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
100 #if 'pp' in str($outputs).split(",")
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
101 --pp '$pp'
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
102 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
103
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
104 $stdout_verbosity
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
105
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
106 #if str($stdout_verbosity) != "--quiet":
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
107 > '$stdout'
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
108 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
109
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
110 #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",")
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
111 && cp $clustal $clustal_strict
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
112 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
113
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
114 #if 'clustal_strict' in str($outputs).split(",")
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
115 && sed -i '/\^#/d' '$clustal_strict'
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
116 #end if
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
117
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
118 ]]></command>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
119
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
120 <inputs>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
121 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
122 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
123 />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
124 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
125 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
126 />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
127 <conditional name="alignment_mode">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
128 <param name="alignment_mode_selector" type="select" label="Alignment mode"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
129 help="Note that local alignment mode usually requires to turn off
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
130 the 'max-diff' heuristic (maximal difference for alignment traces)."
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
131 >
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
132 <option value="global_locarna">Global alignment
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
133 (LocARNA)</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
134 <option value="local_locarna">Local alignment (LocARNA)</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
135 <option value="sparse">Global alignment (SPARSE)</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
136 <option value="structure_sequence_local_locarna">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
137 Structure and sequence local alignment (LocARNA)
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
138 </option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
139 <option value="structure_local_locarna">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
140 Structure local, sequence global alignment (LocARNA)
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
141 </option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
142 </param>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
143 <when value="global_locarna">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
144 <param name="free_endgaps" type="select" label="Free endgaps"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
145 help="Specify whether gaps at the ends (all, 5', or 3' ends)
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
146 of the sequences should be penalized or allowed for free.">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
147 <option value="----">None</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
148 <option value="++++">All</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
149 <option value="+-+-">5' ends</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
150 <option value="-+-+">3' ends</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
151 <option value="++--">first sequence</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
152 <option value="--++">second sequence</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
153 <option value="+---">sequence A, 5' end</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
154 <option value="-+--">sequence A, 3' end</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
155 <option value="--+-">sequence B, 5' end</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
156 <option value="---+">sequence B, 3' end</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
157 </param>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
158 </when>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
159 <when value="local_locarna">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
160 </when>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
161 <when value="sparse" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
162 <when value="structure_sequence_local_locarna" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
163 <when value="structure_local_locarna" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
164 </conditional>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
165
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
166 <param name="outputs" type="select" display="checkboxes" multiple="True"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
167 label="Output options">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
168 <option value="clustal_strict" selected="True">Output alignment
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
169 in ClustalW format</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
170 <option value="clustal" selected="False">Output alignment
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
171 in constraint-annotated ClustalW format</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
172 <option value="stockholm" selected="False">Output
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
173 alignment in Stockholm format</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
174 <option value="pp" selected="False">Output
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
175 alignment in LocARNA's PP 2.0 format</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
176 </param>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
177
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
178 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
179 <option value="--quiet">Don't report standard
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
180 output</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
181 <option value="">Non verbose</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
182 <option value="--verbose">Verbose</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
183 </param>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
184
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
185 <section name="Scoring" title="Scoring parameters">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
186 <expand macro="common_scoring_parameters" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
187 </section>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
188
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
189 <section name="Folding" title="RNA folding parameters">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
190 <expand macro="common_folding_parameters" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
191 <expand macro="alifold_consensus_parameter" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
192 <param name="consensus_structure" type="select" label="Consensus structure type"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
193 help="Type of consensus structures written to screen and stockholm output"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
194 >
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
195 <!-- <option value="mea">mea</option>-->
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
196 <option value="none">none</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
197 <option value="alifold">alifold</option>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
198 </param>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
199 </section>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
200
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
201 <section name="Heuristics" title="Heuristic parameters">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
202 <expand macro="common_heuristic_parameters" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
203 </section>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
204
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
205 <section name="Constraint" title="Constraint parameters">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
206 <expand macro="constraints" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
207 </section>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
208 </inputs>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
209
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
210 <outputs>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
211 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
212 <filter>stdout_verbosity != '--quiet'</filter>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
213 </data>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
214 <data format="clustal" name="clustal"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
215 label="${tool.name} alignment (annotated clustal) on ${on_string}">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
216 <filter>'clustal' in outputs</filter>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
217 </data>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
218 <data format="clustal" name="clustal_strict"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
219 label="${tool.name} alignment (clustal) on ${on_string}">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
220 <filter>'clustal_strict' in outputs</filter>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
221 </data>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
222 <data format="stockholm" name="stockholm"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
223 label="${tool.name} alignment (stockholm) on ${on_string}">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
224 <filter>'stockholm' in outputs</filter>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
225 </data>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
226 <data format="txt" name="pp"
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
227 label="${tool.name} alignment (PP 2.0) on ${on_string}">
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
228 <filter>'pp' in outputs</filter>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
229 </data>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
230 </outputs>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
231
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
232 <tests>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
233 <test>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
234 <param name="inputA" value="tRNA_2-1.fa" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
235 <param name="inputB" value="tRNA_2-2.fa" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
236 <param name="outputs" value="clustal" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
237 <output name="clustal" file="tRNA_2.aln" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
238 </test>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
239 </tests>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
240
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
241 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs**
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
242
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
243 Pairwise RNA alignment tools of the LocARNA suite (locarna,
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
244 sparse). These tools perform variants of simultaneous RNA folding and
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
245 alignment. They can be adapted to specific needs by a broad range of
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
246 parameters:
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
247
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
248 * *scoring* of the alignment, e.g. influencing the cost of
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
249 insertions/deletions and the weight of sequence vs. structure
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
250 similarity.
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
251
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
252 * *RNA folding*, which control the secondary RNA structure prediciton.
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
253
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
254 * *heuristics*, which trade alignment accuracy vs. computation
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
255 speed. The huge complexity of simultaneous alignment and folding
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
256 generally requires some heuristics for reasonable computation times.
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
257 Some alignment instances and alignment modes will require relaxation
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
258 of the default heuristics; in particular, local, constrained, and free end gap
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
259 alignment, will often require turning off the "maximal difference for
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
260 alignment traces" heuristic.
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
261
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
262 * *constraints*, which can be applied to include prior knowledge to
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
263 improve the quality of results and/or speed of computation.
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
264
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
265 **Input.**
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
266
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
267 Input consists of two sequences or alignments, which are specified in
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
268 fasta, clustal, stockholm, or LocARNA pp format.
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
269
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
270 Optionally, one can specify structure and anchor constraints in these
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
271 input files.
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
272
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
273 **Output.**
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
274
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
275 The final pairwise alignment is reported in standard and/or variants of the
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
276 clustal and stockholm format, as well as LocARNA's own pp format.
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
277
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
278 For more information, see
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
279 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
280 ]]></help>
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
281
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
282 <expand macro="citations" />
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
283
b4310d79bbfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
284 </tool>