annotate locarna_best_subtree.xml @ 9:c45eef4517d9 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust commit 4406735e44aba20859c252be39f4e99df28c7a92
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date Sat, 27 Oct 2018 13:24:41 -0400
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1 <tool id="locarna_best_subtree" name="locarna_graphclust" version="0.4" >
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2 <requirements>
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3 <requirement type="package" version="0.6.0">graphclust-wrappers</requirement>
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4 <requirement type="package" version='1.8.10'>locarna</requirement>
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5 <requirement type="package" version='2.1'>rnaz</requirement>
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6 <requirement type="package" version='0.07'>perl-math-round</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command>
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12 <![CDATA[
0
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14 locARNAGraphClust.pl
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15 '$center_fa_file'
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16 '$tree_file'
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17 '$tree_matrix'
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18 '$data_map'
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19 $allow_overlap
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20 $free_endgaps
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21
1
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22 #if str($param_type.param_type_selector) == "gclust"
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23 $param_type.p
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24 $param_type.max_diff_am
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25 $param_type.max_diff
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26 $param_type.tau
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27 $param_type.plfold_minlen
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28 $param_type.struct_weight
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29 $param_type.indel_opening
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30 $param_type.indel
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31 $param_type.alifold_consensus_dp
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32 $param_type.plfold_span
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33 $param_type.plfold_winsize
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34 #end if
0
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35 ]]>
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36 </command>
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37 <inputs>
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38 <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />
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39 <param type="data" name="tree_file" label="trees" format="text" help="text format" />
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40 <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" />
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41 <param type="data" name="data_map" label="data_map" format="txt" help="text format" />
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42 <param name="allow_overlap" type="boolean" truevalue="1" falsevalue="0" label="Allow overlap in subtrees" help="otherwise ignore subtree if it contains overlapping sequences"/>
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43
4
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44 <param name="free_endgaps" type="select" label="Free endgaps"
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45 help="Specify whether gaps at the ends (all, 5', or 3' ends)
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46 of the sequences should be penalized or allowed for free.">
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47 <option value="0">No free endgaps</option>
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48 <option value="--free-endgaps">Free endgaps</option>
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49 <option value="--free-endgaps-5">Free endgaps, only 5'</option>
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50 <option value="--free-endgaps-3">Free endgaps, only 3'</option>
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51 </param>
4
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52 <conditional name="param_type">
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53 <param name="param_type_selector" type="select" label="Choose the type of parameters">
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54 <option value="locarna">LocARNA defaults</option>
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55 <option value="gclust" selected="True">GrapClust defaults(changeable)</option>
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56 </param>
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57 <when value="gclust">
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58 <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
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59 <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>
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60 <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/>
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61 <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
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62 <param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" />
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63 <param name="struct_weight" argument="struct-weight"
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64 label="Structure weight" type="integer"
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65 value="180" min="0" max="800" />
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66 <param name="indel_opening" argument="indel-opening"
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67 label="Indel opening score" type="integer"
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68 value="-400" max="0" min="-1500" />
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69 <param argument="indel" label="Indel score" type="integer"
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70 value="-200" min="-1000" max="0" />
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71 <param name="alifold_consensus_dp"
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72 type="boolean" checked="True"
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73 truevalue="--alifold-consensus-dp" falsevalue=" "
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74 label="Compute consensus dot plot by alifold" />
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75 <param name="plfold_span"
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76 type="integer" value="150" min="-1" max="400"
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77 label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
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78 <param name="plfold_winsize"
1
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79 type="integer" value="300" min="-1" max="800"
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80 label="Window size for local folding" />
4
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81 </when>
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82 <when value="locarna" />
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83 </conditional>
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84 </inputs>
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85 <outputs>
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86 <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />
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87 </outputs>
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88 <tests>
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89 <test>
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90 <param name="tree_file" value="1.1.tree"/>
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91 <param name="center_fa_file" value="1.1.center.fa"/>
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92 <param name="data_map" value="data.map"/>
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93 <param name="tree_matrix" value="1.1.matrix.tree"/>
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94 <param name="allow_overlap" value="0"/>
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95 <param name="free_endgaps" value="0"/>
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96 <param name="param_type_selector" value="gclust"/>
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97 <param name="p" value="0.001"/>
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98 <param name="max_diff_am" value="50"/>
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99 <param name="tau" value="50"/>
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100 <param name="max_diff" value="100"/>
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101 <param name="plfold_minlen" value="210"/>
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102 <param name="struct_weight" value="180"/>
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103 <param name="indel_opening" value="-400"/>
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104 <param name="indel" value="-200"/>
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105 <param name="alifold_consensus_dp" value="--alifold-consensus-dp"/>
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106 <param name="plfold_span" value="150"/>
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107 <param name="plfold_winsize" value="300"/>
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108 <output name="model_tree_stk" file="best_subtree.aln"/>
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109 </test>
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110 </tests>
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111 <help>
1
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112 <![CDATA[
0
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113 **What it does**
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114
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115 MLocARNA computes a multiple sequence-structure alignment of RNA sequences.
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116 It uses *treefile* - file with guide tree in NEWICK format. The given tree is used as guide tree for the progressive alignment.
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117 This saves the calculation of pairwise all-vs-all similarities and construction of the guide tree.
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118
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119
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120 ]]>
1
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121 </help>
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122 <citations>
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123 <citation type="bibtex">@inproceedings{costa2010fast,
0
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124 title={Fast neighborhood subgraph pairwise distance kernel},
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125 author={Costa, Fabrizio and De Grave, Kurt},
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126 booktitle={Proceedings of the 26th International Conference on Machine Learning},
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127 pages={255--262},
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128 year={2010},
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129 organization={Omnipress}
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130 }
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131 </citation>
4
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132 <citation type="doi">10.1261/rna.029041.111</citation>
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133 <citation type="doi">10.1371/journal.pcbi.0030065</citation>
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134 <citation type="doi">10.1093/nar/gkq316</citation>
1
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135 </citations>
0
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136 </tool>