Mercurial > repos > rnateam > locarna_pairwise

annotate locarna_pairwise.xml @ 1:b06dc2bb3716 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
author rnateam
date Fri, 13 Jan 2017 16:49:33 -0500
parents 6a79a086fa50
children 433601e9f132
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b06dc2bb3716 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_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.1">
0
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2 <description>
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3 Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse)
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4 </description>
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5
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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
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10 <expand macro="requirements" />
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11
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12 <expand macro="stdio" />
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13
6a79a086fa50 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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16 <command><![CDATA[
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17 #if str($alignment_mode.alignment_mode_selector) == "sparse"
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18 sparse
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19 #else
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20 locarna
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21 #end if
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23 '$inputA'
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24 '$inputB'
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25
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26 --width 60
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27
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28 ## -------------------- alignment mode and specific options
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29
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30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
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31 #if str($alignment_mode.free_endgaps) != "----"
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32 --free-endgaps $alignment_mode.free_endgaps
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33 #end if
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34 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
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35 --sequ-local on
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36 #else if str($alignment_mode.alignment_mode_selector) == "structure_local_locarna"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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37 --struct-local on
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38 #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna"
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39 --sequ-local on
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40 --struct-local on
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41 #end if
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42
1
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43 @SCORING_ARGS@
0
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44
1
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45 @FOLDING_ARGS@
0
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46 $Folding.alifold_consensus_dp
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47 --consensus-structure $Folding.consensus_structure
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48
1
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49 @HEURISTIC_ARGS@
0
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50
1
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51 @CONSTRAINT_ARGS@
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52
0
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53 ## -------------------- output
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54
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55 #if 'stockholm' in str($outputs).split(",")
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56 --stockholm '$stockholm'
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57 #end if
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58 #if 'clustal' in str($outputs).split(",")
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59 --clustal '$clustal'
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60 #end if
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61 #if 'clustal_strict' in str($outputs).split(",") and (not 'clustal' in str($outputs).split(","))
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62 --clustal '$clustal_strict'
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63 #end if
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64 #if 'pp' in str($outputs).split(",")
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65 --pp '$pp'
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66 #end if
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67
1
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68 @STDOUT_ARGS@
0
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69
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70 #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",")
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71 && cp $clustal $clustal_strict
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72 #end if
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73
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74 #if 'clustal_strict' in str($outputs).split(",")
1
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75 && cp '$clustal_strict' '$clustal_strict~'
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76 && sed '/^#/d' '$clustal_strict~' >'$clustal_strict'
0
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77 #end if
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78
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79 ]]></command>
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80
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81 <inputs>
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82 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
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83 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
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84 />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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85 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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86 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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87 />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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88 <conditional name="alignment_mode">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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89 <param name="alignment_mode_selector" type="select" label="Alignment mode"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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90 help="Note that local alignment mode usually requires to turn off
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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91 the 'max-diff' heuristic (maximal difference for alignment traces)."
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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92 >
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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93 <option value="global_locarna">Global alignment
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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94 (LocARNA)</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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95 <option value="local_locarna">Local alignment (LocARNA)</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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96 <option value="sparse">Global alignment (SPARSE)</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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97 <option value="structure_sequence_local_locarna">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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98 Structure and sequence local alignment (LocARNA)
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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99 </option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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100 <option value="structure_local_locarna">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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101 Structure local, sequence global alignment (LocARNA)
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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102 </option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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103 </param>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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104 <when value="global_locarna">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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105 <param name="free_endgaps" type="select" label="Free endgaps"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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106 help="Specify whether gaps at the ends (all, 5', or 3' ends)
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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107 of the sequences should be penalized or allowed for free.">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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108 <option value="----">None</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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109 <option value="++++">All</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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110 <option value="+-+-">5' ends</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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111 <option value="-+-+">3' ends</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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112 <option value="++--">first sequence</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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113 <option value="--++">second sequence</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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114 <option value="+---">sequence A, 5' end</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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115 <option value="-+--">sequence A, 3' end</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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116 <option value="--+-">sequence B, 5' end</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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117 <option value="---+">sequence B, 3' end</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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118 </param>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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119 </when>
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120 <when value="local_locarna">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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121 </when>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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122 <when value="sparse" />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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123 <when value="structure_sequence_local_locarna" />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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124 <when value="structure_local_locarna" />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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125 </conditional>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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126
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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127 <param name="outputs" type="select" display="checkboxes" multiple="True"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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128 label="Output options">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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129 <option value="clustal_strict" selected="True">Output alignment
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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130 in ClustalW format</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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131 <option value="clustal" selected="False">Output alignment
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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132 in constraint-annotated ClustalW format</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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133 <option value="stockholm" selected="False">Output
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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134 alignment in Stockholm format</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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135 <option value="pp" selected="False">Output
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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136 alignment in LocARNA's PP 2.0 format</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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137 </param>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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138
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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139 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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140 <option value="--quiet">Don't report standard
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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141 output</option>
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142 <option value="">Non verbose</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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143 <option value="--verbose">Verbose</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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144 </param>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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145
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146 <section name="Scoring" title="Scoring parameters">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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147 <expand macro="common_scoring_parameters" />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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148 </section>
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149
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150 <section name="Folding" title="RNA folding parameters">
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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151 <expand macro="common_folding_parameters" />
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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152 <expand macro="alifold_consensus_parameter" />
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153 <param name="consensus_structure" type="select" label="Consensus structure type"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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154 help="Type of consensus structures written to screen and stockholm output"
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155 >
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156 <!-- <option value="mea">mea</option>-->
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157 <option value="none">none</option>
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158 <option value="alifold">alifold</option>
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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159 </param>
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160 </section>
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161
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162 <section name="Heuristics" title="Heuristic parameters">
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163 <expand macro="common_heuristic_parameters" />
1
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164 <expand macro="max_diff_parameters_aln" />
0
6a79a086fa50 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
1
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167 <section name="Constraints" title="Constraint parameters">
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168 <expand macro="common_constraint_parameters" />
0
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169 </section>
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170 </inputs>
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171
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172 <outputs>
1
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173 <expand macro="standard_outupt" />
0
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174 <data format="clustal" name="clustal"
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175 label="${tool.name} alignment (annotated clustal) on ${on_string}">
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176 <filter>'clustal' in outputs</filter>
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177 </data>
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178 <data format="clustal" name="clustal_strict"
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179 label="${tool.name} alignment (clustal) on ${on_string}">
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180 <filter>'clustal_strict' in outputs</filter>
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181 </data>
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182 <data format="stockholm" name="stockholm"
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183 label="${tool.name} alignment (stockholm) on ${on_string}">
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184 <filter>'stockholm' in outputs</filter>
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185 </data>
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186 <data format="txt" name="pp"
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187 label="${tool.name} alignment (PP 2.0) on ${on_string}">
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188 <filter>'pp' in outputs</filter>
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189 </data>
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190 </outputs>
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191
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192 <tests>
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193 <test>
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194 <param name="inputA" value="tRNA_2-1.fa" />
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195 <param name="inputB" value="tRNA_2-2.fa" />
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196 <param name="outputs" value="clustal" />
1
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197 <output name="clustal" file="tRNA_2.aln" lines_diff="2" />
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198 </test>
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199 <test>
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200 <param name="inputA" value="haca.snoRNA-1.aln" />
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201 <param name="inputB" value="haca.snoRNA-2.aln" />
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202 <param name="outputs" value="clustal_strict,clustal" />
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203 <output name="clustal" file="haca.snoRNA-c.aln" lines_diff="2" />
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204 <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="1" />
0
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205 </test>
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206 </tests>
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207
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208 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs**
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209
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210 Pairwise RNA alignment tools of the LocARNA suite (locarna,
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211 sparse). These tools perform variants of simultaneous RNA folding and
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212 alignment. They can be adapted to specific needs by a broad range of
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213 parameters:
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214
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215 * *scoring* of the alignment, e.g. influencing the cost of
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216 insertions/deletions and the weight of sequence vs. structure
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217 similarity.
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218
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219 * *RNA folding*, which control the secondary RNA structure prediciton.
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220
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221 * *heuristics*, which trade alignment accuracy vs. computation
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222 speed. The huge complexity of simultaneous alignment and folding
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223 generally requires some heuristics for reasonable computation times.
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224 Some alignment instances and alignment modes will require relaxation
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225 of the default heuristics; in particular, local, constrained, and free end gap
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226 alignment, will often require turning off the "maximal difference for
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227 alignment traces" heuristic.
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228
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229 * *constraints*, which can be applied to include prior knowledge to
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230 improve the quality of results and/or speed of computation.
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231
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232 **Input.**
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233
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234 Input consists of two sequences or alignments, which are specified in
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235 fasta, clustal, stockholm, or LocARNA pp format.
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236
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237 Optionally, one can specify structure and anchor constraints in these
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238 input files.
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239
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240 **Output.**
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241
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242 The final pairwise alignment is reported in standard and/or variants of the
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243 clustal and stockholm format, as well as LocARNA's own pp format.
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244
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245 For more information, see
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246 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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247 ]]></help>
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248
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249 <expand macro="citations" />
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250
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251 </tool>