Mercurial > repos > rnateam > graphclust_mlocarna

annotate locarna_best_subtree.xml @ 1:f073950f2217 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author rnateam
date Sat, 21 Jan 2017 17:25:45 -0500
parents 8785bca2c1f2
children 54c44d1617fe
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8785bca2c1f2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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1 <tool id="locarna_best_subtree" name="locarna_best_subtree" version="0.1.0" >
1
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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2 <requirements>
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3 <requirement type="package" version="0.1.7">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:" />
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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10 </stdio>
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11 <command>
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12 <![CDATA[
0
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13
1
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14 'locARNAGraphClust.pl' '$center_fa_file' '$tree_file' '$tree_matrix' '$data_map'
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15 #if str($param_type.param_type_selector) == "gclust"
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16 $param_type.p
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17 $param_type.max_diff_am
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18 $param_type.max_diff
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19 $param_type.tau
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20 $param_type.plfold_minlen
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21 $param_type.struct_weight
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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22 $param_type.indel_opening
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23 $param_type.indel
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24 $param_type.alifold_consensus_dp
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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25 $param_type.plfold_span
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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26 $param_type.plfold_winsize
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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27 #end if
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28 ]]>
1
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29 </command>
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30 <inputs>
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31 <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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32 <param type="data" name="tree_file" label="trees" format="text" help="text format" />
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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33 <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" />
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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34 <param type="data" name="data_map" label="data_map" format="txt" help="text format" />
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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35
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37 <conditional name="param_type">
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38 <param name="param_type_selector" type="select" label="Choose the type of parameters">
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39 <option value="locarna">LocARNA defaults</option>
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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40 <option value="gclust" selected="True">GrapClust defaults(changeable)</option>
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41 </param>
f073950f2217 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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42 <when value="gclust">
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43
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44 <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
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45 <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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46 <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/>
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47 <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
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48 <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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49
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50 <param name="struct_weight" argument="struct-weight"
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51 label="Structure weight" type="integer"
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52 value="180" min="0" max="800" />
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53 <param name="indel_opening" argument="indel-opening"
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54 label="Indel opening score" type="integer"
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55 value="-400" max="0" min="-1500" />
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56 <param argument="indel" label="Indel score" type="integer"
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57 value="-200" min="-1000" max="0" />
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58
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59 <param name="alifold_consensus_dp"
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60 type="boolean" checked="True"
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61 truevalue="--alifold-consensus-dp" falsevalue=" "
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62 label="Compute consensus dot plot by alifold" />
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63
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64 <param name="plfold_span"
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65 type="integer" value="150" min="-1" max="400"
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66 label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
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67
1
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68 <param name="plfold_winsize"
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69 type="integer" value="300" min="-1" max="800"
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70 label="Window size for local folding" />
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72
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73 </when>
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74 <when value="locarna">
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75 </when>
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76 </conditional>
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77
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78 </inputs>
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79 <outputs>
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80
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81 <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="tree_file" value="1.1.tree"/>
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86 <param name="center_fa_file" value="1.1.center.fa"/>
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87 <param name="data_map" value="data.map"/>
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88 <param name="tree_matrix" value="1.1.matrix.tree"/>
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89 <conditional name="param_type">
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90 <param name="iteration_num_selector" value="gclust"/>
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91 <param name="p" value="0.001"/>
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92 <param name="max_diff_am" value="50"/>
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93 <param name="tau" value="50"/>
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94 <param name="max_diff" value="100"/>
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95 <param name="plfold_minlen" value="210"/>
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96 <param name="struct_weight" value="180"/>
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97 <param name="indel_opening" value="-400"/>
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98 <param name="indel" value="-200"/>
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99 <param name="alifold_consensus_dp" value="--alifold-consensus-dp"/>
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100 <param name="plfold_span" value="150"/>
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101 <param name="plfold_winsize" value="300"/>
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102 </conditional>
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103 <output name="model_tree_stk" file="best_subtree.aln"/>
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104 </test>
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105 </tests>
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106 <help>
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107 <![CDATA[
0
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108 **What it does**
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109
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110 MLocARNA computes a multiple sequence-structure alignment of RNA sequences.
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111 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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112 This saves the calculation of pairwise all-vs-all similarities and construction of the guide tree.
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113
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114
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115
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116 ]]>
1
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117 </help>
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118 <citations>
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119 <citation type="bibtex">@inproceedings{costa2010fast,
0
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120 title={Fast neighborhood subgraph pairwise distance kernel},
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121 author={Costa, Fabrizio and De Grave, Kurt},
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122 booktitle={Proceedings of the 26th International Conference on Machine Learning},
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123 pages={255--262},
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124 year={2010},
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125 organization={Omnipress}
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126 }
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127 </citation>
1
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128 <citation type="bibtex">@Article{Will_Joshi_Hofacker-LocAR_Accur_bound-2012,
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129 author = {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and
0
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130 Stadler, Peter F. and Backofen, Rolf},
1
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131 title = {{LocARNA}-{P}: {Accurate} boundary prediction and improved
0
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132 detection of structural {RNAs}},
1
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133 journal = {RNA},
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134 year = {2012},
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135 volume = {18},
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136 number = {5},
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137 pages = {900-14},
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138 user = {will},
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139 pmid = {22450757},
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140 doi = {10.1261/rna.029041.111},
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141 issn = {1469-9001},
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142 issn = {1355-8382},
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143 abstract = {Current genomic screens for noncoding RNAs (ncRNAs) predict
0
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144 a large number of genomic regions containing potential
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145 structural ncRNAs. The analysis of these data requires
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146 highly accurate prediction of ncRNA boundaries and
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147 discrimination of promising candidate ncRNAs from weak
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148 predictions. Existing methods struggle with these goals
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149 because they rely on sequence-based multiple sequence
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150 alignments, which regularly misalign RNA structure and
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151 therefore do not support identification of structural
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152 similarities. To overcome this limitation, we compute
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153 columnwise and global reliabilities of alignments based on
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154 sequence and structure similarity; we refer to these
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155 structure-based alignment reliabilities as STARs. The
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156 columnwise STARs of alignments, or STAR profiles, provide a
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157 versatile tool for the manual and automatic analysis of
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158 ncRNAs. In particular, we improve the boundary prediction of
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159 the widely used ncRNA gene finder RNAz by a factor of 3 from
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160 a median deviation of 47 to 13 nt. Post-processing RNAz
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161 predictions, LocARNA-P's STAR score allows much stronger
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162 discrimination between true- and false-positive predictions
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163 than RNAz's own evaluation. The improved accuracy, in this
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164 scenario increased from AUC 0.71 to AUC 0.87, significantly
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165 reduces the cost of successive analysis steps. The
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166 ready-to-use software tool LocARNA-P produces
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167 structure-based multiple RNA alignments with associated
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168 columnwise STARs and predicts ncRNA boundaries. We provide
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169 additional results, a web server for LocARNA/LocARNA-P, and
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170 the software package, including documentation and a pipeline
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171 for refining screens for structural ncRNA, at
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172 http://www.bioinf.uni-freiburg.de/Supplements/LocARNA-P/.}
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173 }
1
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174 </citation>
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175 <citation type="bibtex">@Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007,
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176 author = {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and
0
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177 Peter F. Stadler and Rolf Backofen},
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178 title = {Inferring Non-Coding {RNA} Families and Classes by Means of
0
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179 Genome-Scale Structure-Based Clustering},
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180 journal = {PLoS Comput Biol},
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181 year = 2007,
0
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182 volume = {3},
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183 number = {4},
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184 pages = {e65},
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185 issn = {1553-7358},
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186 issn = {1553-734X},
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187 pmid = {17432929},
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188 doi = {10.1371/journal.pcbi.0030065},
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189 user = {will},
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190 abstract = {The RFAM database defines families of ncRNAs by means of
0
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191 sequence similarities that are sufficientto establish
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192 homology. In some cases, such as microRNAs, box H/ACA
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193 snoRNAs, functional commonalities define classes of RNAs
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194 that are characterized by structural similarities, and
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195 typically consist ofmultiple RNA families. Recent advances
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196 in high-throughput transcriptomics and comparative genomics
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197 have produced very large sets of putative non-coding RNAs
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198 and regulatory RNA signals. For many ofthem, evidence for
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199 stabilizing selection acting on their secondary structures
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200 has been derived, and at least approximate models of their
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201 structures have been computed. The overwhelming majority of
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202 these hypo-thetical RNAs cannot be assigned to established
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203 families or classes. We present here a structure-based
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204 clustering approach that is capable of extracting putative
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205 RNA classesfrom genome-wide surveys for structured RNAs. The
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206 LocARNA tool implements a novel variant of theSankoff
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207 algorithm that is sufficiently fast to deal with several
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208 thousand candidate sequences. The method is also robust
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209 against false positive predictions, i.e., a contamination of
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210 the input data with unstructured ornon-conserved
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211 sequences. We have successfully tested the LocARNA-based
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212 clustering approach on the sequences of the
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213 RFAM-seedalignments. Furthermore, we have applied it to a
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214 previously published set of 3332 predicted structured
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215 elements in the Ciona intestinalis genomes (Missal et al.,
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216 Bioinformatics 21(S2), i77-i78). In addition torecovering
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217 e.g. tRNAs as a structure-based class, the method identifies
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218 several RNA families, including microRNA and snoRNA
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219 candidates, and suggests several novel classes of ncRNAs for
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220 which to-date norepresentative has been experimentally
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221 characterized.}
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222 }
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223
1
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224 </citation>
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225 <citation type="bibtex">@Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010,
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226 author = {Smith, Cameron and Heyne, Steffen and Richter, Andreas S.
0
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227 and Will, Sebastian and Backofen, Rolf},
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228 title = {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA},
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229 {ExpaRNA} and {LocARNA}},
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230 journal = NAR,
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231 year = {2010},
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232 volume = {38 Suppl},
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233 number = {},
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234 pages = {W373-7},
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235 user = {arichter},
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236 pmid = {20444875},
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237 doi = {10.1093/nar/gkq316},
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238 issn = {0305-1048},
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239 issn = {1362-4962},
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240 abstract = {The Freiburg RNA tools web server integrates three tools
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241 for the advanced analysis of RNA in a common web-based user
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242 interface. The tools IntaRNA, ExpaRNA and LocARNA support
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243 the prediction of RNA-RNA interaction, exact RNA matching
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244 and alignment of RNA, respectively. The Freiburg RNA tools
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245 web server and the software packages of the stand-alone
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246 tools are freely accessible at
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247 http://rna.informatik.uni-freiburg.de.}
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248 }
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249 </citation>
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250 </citations>
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251 </tool>