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annotate mlocarna.xml @ 0:59055c49a112 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author rnateam
date Tue, 06 Dec 2016 11:39:14 -0500
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59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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1 <tool id="mlocarna" name="LocARNA" version="@VERSION@.0">
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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2 <description>
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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3 Multiple Alignment and Folding of RNAs
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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4 </description>
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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6 <macros>
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7 <import>macros.xml</import>
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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8 </macros>
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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9
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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10 <expand macro="requirements" />
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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12 <expand macro="stdio" />
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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14 <expand macro="version" />
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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16 <command><![CDATA[
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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17 mlocarna
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19 '$input_data'
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20 #if 'stockholm' in str($outputs).split(","):
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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21 --stockholm
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22 #end if
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24 --tgtdir 'outdir'
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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26 ## -------------------- alignment mode and specific options
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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27
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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28 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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29 $alignment_mode.free_endgaps
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30 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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31 --sequ-local on
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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32 #else if str($alignment_mode.alignment_mode_selector) == "probabilistic"
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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33 --probabilistic
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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34 $alignment_mode.consistency_transformation
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35
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36 #if str($alignment_mode.iterate) == "true"
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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37 --iterate
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38 --iterations $alignment_mode.iterations
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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39 #end if
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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40 #else if str($alignment_mode.alignment_mode_selector) == "sparse"
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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41 --sparse
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42 #end if
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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43
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44 ## -------------------- scoring parameters
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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45
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46 --indel $Scoring.indel
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47 --indel-opening $Scoring.indel_opening
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48 --struct-weight $Scoring.struct_weight
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49 --tau $Scoring.tau
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50
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51 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
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52 --match $Scoring.sequence_score.match
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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53 --mismatch $Scoring.sequence_score.mismatch
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54 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
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55 --use-ribosum true
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56 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
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57 --ribofit true
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58 #end if
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59
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60 ## -------------------- folding parameters
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61
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62 #if $Folding.plfold_span>=0
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63 --plfold-span $Folding.plfold_span
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64 --plfold-winsize $Folding.plfold_winsize
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65 #end if
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66
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67 --rnafold-temperature $Folding.rnafold_temperature
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68
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69 ## -------------------- heuristic parameters
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70
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71 -p $Heuristics.min_prob
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72 --max-diff-am $Heuristics.max_diff_am
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73 --max-diff $Heuristics.max_diff
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74 --max-diff-at-am $Heuristics.max_diff_at_am
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75 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
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76
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77 $Heuristics.alifold_consensus_dp
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78
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79 ## -------------------- other parameters
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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80
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81 $Other.lonely_pairs
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82
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83 $stdout_verbosity
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84
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85 #if str($stdout_verbosity) != "--quiet":
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86 > '$stdout'
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87 #end if
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88 ]]></command>
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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89
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90 <inputs>
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91 <param name="input_data" type="data" format="text,fasta" label="Sequence input"
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92 help="Sequence input in fasta format, optionally with locarna-specific extensions"
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93 />
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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94
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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95 <conditional name="alignment_mode">
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96 <param name="alignment_mode_selector" type="select" label="Alignment mode">
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97 <option value="global_locarna">Global alignment (LocARNA)</option>
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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98 <option value="local_locarna">Local alignment (LocARNA)</option>
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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99 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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100 <option value="sparse">Global alignment (SPARSE)</option>
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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101 </param>
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102 <when value="global_locarna">
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103 <param name="free_endgaps" type="select" label="Free endgaps">
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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104 <option value="">No free endgaps</option>
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105 <option value="--free-endgaps">Free endgaps</option>
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106 <option value="--free-endgaps-5">Free endgaps, only 5'</option>
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107 <option value="--free-endgaps-3">Free endgaps, only 3'</option>
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108 </param>
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109 </when>
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110 <when value="local_locarna" />
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111 <when value="probabilistic">
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112 <param name="consistency_transformation" type="boolean"
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113 truevalue="--consistency-transformation" falsevalue=""
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114 checked="true" label="Consistency transformation"
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115 help="--consistency-transformation" />
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116 <param name="iterate" type="boolean"
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117 truevalue="true" falsevalue="false"
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118 checked="false" label="Iterative refinement"
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119 help="--iterate" />
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120 <param name="iterations" type="integer"
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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121 value="1" label="Number of refinement iterations"
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122 help="--iterations num" />
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123 </when>
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124 <when value="sparse" />
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125 </conditional>
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126
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127 <param name="outputs" type="select" display="checkboxes" multiple="True"
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128 label="Output options">
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129 <option value="clustal" selected="True">Output alignment
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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130 in Clustalw format</option>
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131 <option value="stockholm" selected="False">Output
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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132 alignment in Stockholm format</option>
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133 </param>
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134
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135 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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136 <option value="--quiet">Don't report standard
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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137 output</option>
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138 <option value="">Non verbose</option>
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139 <option value="--verbose">Verbose</option>
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140 <option value="--moreverbose">More verbose</option>
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141 </param>
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142
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143
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144 <section name="Scoring" title="Scoring parameters">
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145 <expand macro="common_scoring_parameters" />
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146 </section>
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147
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148 <section name="Folding" title="RNA folding parameters">
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149 <expand macro="common_folding_parameters" />
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150 </section>
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151
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152 <section name="Heuristics" title="Heuristic parameters">
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153 <expand macro="common_heuristic_parameters" />
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154 </section>
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155
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156 <section name="Other" title="Other parameters">
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157 <expand macro="common_other_parameters" />
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158 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP"
59055c49a112 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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159 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
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160 </section>
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161 </inputs>
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162
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163 <outputs>
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164 <expand macro="common_outputs" />
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165 </outputs>
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166
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167 <tests>
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168 <test>
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169 <param name="input_data" value="archaea.fa" />
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170 <param name="stdout_verbosity" value="" />
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171 <output name="stdout" file="archaea-default.stdout" />
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172 </test>
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173 <test>
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174 <param name="input_data" value="haca.snoRNA.fa" />
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175 <param name="stdout_verbosity" value="" />
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176 <output name="stdout" file="haca.snoRNA-default.stdout" />
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177 </test>
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178 <test>
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179 <param name="input_data" value="archaea.fa" />
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180 <param name="stdout_verbosity" value="" />
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181 <param name="outputs" value="clustal" />
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182 <param name="alignment_mode_selector" value="probabilistic" />
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183 <output name="clustal" file="archaea-probabilistic.aln" />
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184 </test>
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185 </tests>
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186
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187 <help><![CDATA[ **Multiple alignment of RNAs**
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188
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189 For more information, see
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190 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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191 ]]></help>
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192
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193 <expand macro="citations" />
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194
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195 </tool>