Mercurial > repos > rnateam > locarna_multiple

annotate locarna_multiple.xml @ 2:f8c5261fafdc draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author rnateam
date Sat, 21 Jan 2017 17:22:23 -0500
parents 3a4167720464
children
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3a4167720464 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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1 <tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@VERSION@.1">
0
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2 <description>
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3 Multiple Alignment and Folding of RNAs (mlocarna)
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4 </description>
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86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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10 <expand macro="requirements" />
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86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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12 <expand macro="stdio" />
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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14 <expand macro="version" />
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86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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16 <command><![CDATA[
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17 mlocarna
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19 '$input_data'
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20 #if 'stockholm' in str($outputs).split(","):
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21 --stockholm
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22 #end if
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86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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24 --tgtdir mlocarna_results
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25 --width 60
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27 ## -------------------- alignment mode and specific options
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28 #
0
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29 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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30 $alignment_mode.free_endgaps
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31 #elif str($alignment_mode.alignment_mode_selector) == "local_locarna"
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32 --sequ-local on
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33 #elif str($alignment_mode.alignment_mode_selector) == "probabilistic"
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34 --probabilistic
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35 $alignment_mode.consistency_transformation
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36
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37 #if str($alignment_mode.iterate) == "true"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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38 --iterate
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39 --iterations $alignment_mode.iterations
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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40 #end if
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41 #elif str($alignment_mode.alignment_mode_selector) == "sparse"
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42 --sparse
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43 #end if
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44
1
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45 @SCORING_ARGS@
0
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46
1
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47 @FOLDING_ARGS@
0
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48 #if $Folding.plfold_span>=0
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49 --plfold-span $Folding.plfold_span
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50 --plfold-winsize $Folding.plfold_winsize
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51 #end if
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52 $Folding.alifold_consensus_dp
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53
1
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54 @HEURISTIC_ARGS@
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55
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56 #if str($alignment_mode.alignment_mode_selector) == "sparse"
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57 --pw-aligner-options " @HEURISTIC_SPARSE_ARGS@ "
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58 #end if
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59
0
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60
1
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61 @CONSTRAINT_ARGS@
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62 #if str($Constraints.bed_anchors.bed_anchors_selector) == "yes"
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63 --anchor-constraints $Constraints.bed_anchors.bed_anchors_file
0
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64 #end if
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65
1
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66 @STDOUT_ARGS@
0
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67
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68 #if 'clustal_strict' in str($outputs).split(",")
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69 && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
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70 #end if
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71
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72 ]]></command>
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73
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74 <inputs>
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75 <conditional name="input_data_type">
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76 <param name="input_data_type_selector" type="select" label="Input type">
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77 <option value="fasta">Fasta input (strict)</option>
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78 <option value="text">Fasta-like input with LocARNA constraints</option>
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79 </param>
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80 <when value="fasta">
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81 <param name="input_data" type="data" format="fasta" label="Sequence input"
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82 help="Sequence input in pure fasta format"
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83 />
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84 </when>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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85 <when value="text">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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86 <param name="input_data" type="data" format="text" label="Sequence input"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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87 help="Sequence input in fasta format with locarna-specific extensions"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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88 />
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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89 </when>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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90 </conditional>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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91 <conditional name="alignment_mode">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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92 <param name="alignment_mode_selector" type="select" label="Alignment mode"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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93 help="Note that local alignment mode usually requires to turn off
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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94 the 'max-diff' heuristic (maximal difference for alignment traces)."
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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95 >
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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96 <option value="global_locarna">Global alignment
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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97 (LocARNA)</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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98 <option value="local_locarna">Local alignment (LocARNA)</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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99 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
2
f8c5261fafdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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100 <option value="sparse">Global fast alignment (SPARSE)</option>
0
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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101 </param>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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102 <when value="global_locarna">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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103 <param name="free_endgaps" type="select" label="Free endgaps"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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104 help="Specify whether gaps at the ends (all, 5', or 3' ends)
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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105 of the sequences should be penalized or allowed for free.">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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106 <option value="">No free endgaps</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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107 <option value="--free-endgaps">Free endgaps</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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108 <option value="--free-endgaps-5">Free endgaps, only 5'</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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109 <option value="--free-endgaps-3">Free endgaps, only 3'</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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110 </param>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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111 </when>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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112 <when value="local_locarna">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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113 </when>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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114 <when value="probabilistic">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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115 <param name="consistency_transformation" type="boolean"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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116 truevalue="--consistency-transformation" falsevalue=""
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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117 checked="true" label="Consistency transformation"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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118 help="--consistency-transformation" />
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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119 <param name="iterate" type="boolean"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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120 truevalue="true" falsevalue="false"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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121 checked="false" label="Iterative refinement"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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122 help="--iterate" />
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123 <param name="iterations" type="integer"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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124 value="1" label="Number of refinement iterations"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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125 help="--iterations num" />
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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126 </when>
2
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127 <when value="sparse">
f8c5261fafdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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128 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">
f8c5261fafdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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129 <expand macro="common_heuristic_parameters_sparse" />
f8c5261fafdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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130 </section>
f8c5261fafdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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131 </when>
f8c5261fafdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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132
0
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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133 </conditional>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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134
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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135 <param name="outputs" type="select" display="checkboxes" multiple="True"
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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136 label="Output options">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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137 <option value="clustal_strict" selected="True">Output alignment
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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138 in ClustalW format</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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139 <option value="clustal" selected="False">Output alignment
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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140 in constraint-annotated ClustalW format</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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141 <option value="stockholm" selected="False">Output
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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142 alignment in Stockholm format</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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143 <option value="pp" selected="False">Output
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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144 alignment in LocARNA's PP 2.0 format</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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145 <option value="mlocarna_results" selected="False">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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146 Output LocARNA results archive (tar.gz)</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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147 </param>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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148
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149 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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150 <option value="--quiet">Don't report standard
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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151 output</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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152 <option value="">Non verbose</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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153 <option value="--verbose">Verbose</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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154 <option value="--moreverbose">More verbose</option>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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155 </param>
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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156
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157 <section name="Scoring" title="Scoring parameters">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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158 <expand macro="common_scoring_parameters" />
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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159 </section>
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160
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161 <section name="Folding" title="RNA folding parameters">
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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162 <expand macro="plfolding_parameters" />
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163 <expand macro="common_folding_parameters" />
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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164 <expand macro="alifold_consensus_parameter" />
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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165 </section>
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166
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167 <section name="Heuristics" title="Heuristic parameters">
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168 <expand macro="common_heuristic_parameters" />
1
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169 <expand macro="max_diff_parameters_aln" />
0
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170 </section>
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171
1
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172 <section name="Constraints" title="Constraint parameters">
0
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173 <expand macro="bed_anchors" />
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174 <expand macro="common_constraint_parameters" />
0
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175 </section>
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176 </inputs>
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177
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178 <outputs>
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179 <expand macro="mlocarna_outputs" />
0
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180 </outputs>
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181
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182 <tests>
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183 <test>
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184 <param name="input_data" value="archaea.fa" />
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185 <param name="stdout_verbosity" value="" />
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186 <param name="max_diff_mode_selector" value="max-diff" />
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187 <param name="max_diff" value="20" />
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188 <output name="stdout" file="archaea-default.stdout" />
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189 </test>
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190 <test>
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191 <param name="input_data" value="haca.snoRNA.fa" />
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192 <param name="stdout_verbosity" value="" />
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193 <output name="stdout" file="haca.snoRNA-default.stdout" />
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194 </test>
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195 <test>
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196 <param name="input_data" value="archaea.fa" />
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197 <param name="stdout_verbosity" value="" />
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198 <param name="outputs" value="clustal" />
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199 <param name="alignment_mode_selector" value="probabilistic" />
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200 <output name="clustal" file="archaea-probabilistic.aln" />
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201 </test>
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202 <test>
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203 <param name="input_data" value="archaea.fa" />
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204 <param name="stdout_verbosity" value="" />
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205 <param name="outputs" value="clustal" />
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206 <param name="max_diff_mode_selector" value="max-diff-aln" />
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207 <param name="max_diff_aln" value="archaea-ref.aln" />
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208 <param name="max_diff" value="2" />
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209 <output name="clustal" file="archaea-ref_result.aln" />
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210 </test>
0
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211 </tests>
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212
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213 <help><![CDATA[ **MLocARNA -- Multiple alignment of RNAs**
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214
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215 MLocARNA is the (general, progressive) multiple RNA alignment tool of
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216 the LocARNA suite. It supports several alignment modes and can be
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217 adapted to specific needs by a broad range of parameters. Thus, there
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218 are parameters for
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219
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220 * *scoring* of the alignment, e.g. influencing the cost of
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221 insertions/deletions and the weight of sequence vs. structure
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222 similarity.
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223
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224 * *RNA folding*, which control the secondary RNA structure prediciton.
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225
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226 * *heuristics*, which trade alignment accuracy vs. computation
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227 speed. The huge complexity of simultaneous alignment and folding
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228 generally requires some heuristics for reasonable computation times.
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229 Some alignment instances and alignment modes will require relaxation
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230 of the default heuristics; in particular, local, constrained, and free end gap
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231 alignment, will often require turning off the "maximal difference for
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232 alignment traces" heuristic.
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233
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234 * *constraints*, which can be applied to include prior knowledge to
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235 improve the quality of results and/or speed of computation.
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236
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237 Technically, mlocarna constructs multiple alignments progressively
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238 based on pairwise alignments by locarna, locarna-p, or sparse, which
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239 perform variants of simultaneous RNA folding and alignment.
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240
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241 **Input.**
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242 Sequences can be given in plain fasta format like::
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243
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244 >fruA
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245 CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG
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246 >fdhA
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247 CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG
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248 >vhuU
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249 AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU
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250
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251 Morover, mlocarna supports structure constraints for folding and anchor
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252 constraints for alignment. Both types of constraints can be specified
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253 in extension of the standard fasta format via 'constraint
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254 lines'. Fasta-ish input with constraints looks like this::
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255
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256 >A
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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257 GACCCUGGGAACAUUAACUACUCUCGUUGGUGAUAAGGAACA
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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258 ..((.(....xxxxxx...................))).xxx #S
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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259 ..........000000.......................111 #1
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260 ..........123456.......................123 #2
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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261 >B
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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262 ACGGAGGGAAAGCAAGCCUUCUGCGACA
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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263 .(((....xxxxxx.......))).xxx #S
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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264 ........000000...........111 #1
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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265 ........123456...........123 #2
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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266
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267 The same anchor constraints (like by the lines tagged #1, #2) can
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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268 alternatively be specified in bed format by the entries::
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269
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270 A 10 16 first_box
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271 B 8 14 first_box
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272 A 39 42 ACA-box
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273 B 25 28 ACA-box
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274
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275 where anchor regions (boxes) have arbitrary but matching names
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276 and contig/sequence names correspond to the sequence names
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277 of the fasta(-like) input.
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278
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279
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280 **Output.**
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281
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282 The final alignment is reported in standard and/or variants of the
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283 clustal and stockholm format. Moreover, an archive with final and
86abdf5de84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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284 intermediary results of the mlocarna run can be returned.
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285
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286
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287 For more information, see
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288 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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289 ]]></help>
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290
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291 <expand macro="citations" />
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292
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293 </tool>