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comparison locarna_best_subtree.xml @ 0:15bd4fb05e5c draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
author rnateam
date Fri, 16 Dec 2016 07:35:29 -0500
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1 <tool id="locarna_best_subtree" name="locarna_best_subtree" version="0.1.0" >
2 <requirements>
3 <requirement type="package" version="0.1">graphclust-wrappers</requirement>
4 <requirement type="package" version='1.8.10'>locarna</requirement>
5 <requirement type="package" version='2.1'>rnaz</requirement>
6 <requirement type="package" version='0.07'>perl-math-round</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1:" />
10 </stdio>
11 <command>
12 <![CDATA[
13
14 'locARNAGraphClust.pl' '$center_fa_file' '$tree_file' '$tree_matrix' $p $max_diff_am $tau $max_diff '' '$data_map' $plfold_minlen
15 ]]>
16 </command>
17 <inputs>
18 <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />
19 <param type="data" name="tree_file" label="trees" format="text" help="text format" />
20 <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" />
21 <param type="data" name="data_map" label="data_map" format="txt" help="text format" />
22 <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
23 <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>
24 <param name="tau" type="integer" value="50" size="5" label="Tau factor in percent" help="--tau"/>
25 <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
26 <param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" />
27 </inputs>
28 <outputs>
29
30 <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />
31 </outputs>
32 <tests>
33 <test>
34 <param name="tree_file" value="1.1.tree"/>
35 <param name="center_fa_file" value="1.1.center.fa"/>
36 <param name="data_map" value="data.map"/>
37 <param name="tree_matrix" value="1.1.matrix.tree"/>
38 <param name="p" value="0.001"/>
39 <param name="max-diff-am" value="50"/>
40 <param name="tau" value="50"/>
41 <param name="max-diff-am" value="100"/>
42 <output name="model_tree_stk" file="best_subtree.aln"/>
43 </test>
44 </tests>
45 <help>
46 <![CDATA[
47 **What it does**
48
49 MLocARNA computes a multiple sequence-structure alignment of RNA sequences.
50 It uses *treefile* - file with guide tree in NEWICK format. The given tree is used as guide tree for the progressive alignment.
51 This saves the calculation of pairwise all-vs-all similarities and construction of the guide tree.
52
53
54
55 ]]>
56 </help>
57 <citations>
58 <citation type="bibtex">@inproceedings{costa2010fast,
59 title={Fast neighborhood subgraph pairwise distance kernel},
60 author={Costa, Fabrizio and De Grave, Kurt},
61 booktitle={Proceedings of the 26th International Conference on Machine Learning},
62 pages={255--262},
63 year={2010},
64 organization={Omnipress}
65 }
66 </citation>
67 <citation type="bibtex">@Article{Will_Joshi_Hofacker-LocAR_Accur_bound-2012,
68 author = {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and
69 Stadler, Peter F. and Backofen, Rolf},
70 title = {{LocARNA}-{P}: {Accurate} boundary prediction and improved
71 detection of structural {RNAs}},
72 journal = {RNA},
73 year = {2012},
74 volume = {18},
75 number = {5},
76 pages = {900-14},
77 user = {will},
78 pmid = {22450757},
79 doi = {10.1261/rna.029041.111},
80 issn = {1469-9001},
81 issn = {1355-8382},
82 abstract = {Current genomic screens for noncoding RNAs (ncRNAs) predict
83 a large number of genomic regions containing potential
84 structural ncRNAs. The analysis of these data requires
85 highly accurate prediction of ncRNA boundaries and
86 discrimination of promising candidate ncRNAs from weak
87 predictions. Existing methods struggle with these goals
88 because they rely on sequence-based multiple sequence
89 alignments, which regularly misalign RNA structure and
90 therefore do not support identification of structural
91 similarities. To overcome this limitation, we compute
92 columnwise and global reliabilities of alignments based on
93 sequence and structure similarity; we refer to these
94 structure-based alignment reliabilities as STARs. The
95 columnwise STARs of alignments, or STAR profiles, provide a
96 versatile tool for the manual and automatic analysis of
97 ncRNAs. In particular, we improve the boundary prediction of
98 the widely used ncRNA gene finder RNAz by a factor of 3 from
99 a median deviation of 47 to 13 nt. Post-processing RNAz
100 predictions, LocARNA-P's STAR score allows much stronger
101 discrimination between true- and false-positive predictions
102 than RNAz's own evaluation. The improved accuracy, in this
103 scenario increased from AUC 0.71 to AUC 0.87, significantly
104 reduces the cost of successive analysis steps. The
105 ready-to-use software tool LocARNA-P produces
106 structure-based multiple RNA alignments with associated
107 columnwise STARs and predicts ncRNA boundaries. We provide
108 additional results, a web server for LocARNA/LocARNA-P, and
109 the software package, including documentation and a pipeline
110 for refining screens for structural ncRNA, at
111 http://www.bioinf.uni-freiburg.de/Supplements/LocARNA-P/.}
112 }
113 </citation>
114 <citation type="bibtex">@Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007,
115 author = {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and
116 Peter F. Stadler and Rolf Backofen},
117 title = {Inferring Non-Coding {RNA} Families and Classes by Means of
118 Genome-Scale Structure-Based Clustering},
119 journal = {PLoS Comput Biol},
120 year = 2007,
121 volume = {3},
122 number = {4},
123 pages = {e65},
124 issn = {1553-7358},
125 issn = {1553-734X},
126 pmid = {17432929},
127 doi = {10.1371/journal.pcbi.0030065},
128 user = {will},
129 abstract = {The RFAM database defines families of ncRNAs by means of
130 sequence similarities that are sufficientto establish
131 homology. In some cases, such as microRNAs, box H/ACA
132 snoRNAs, functional commonalities define classes of RNAs
133 that are characterized by structural similarities, and
134 typically consist ofmultiple RNA families. Recent advances
135 in high-throughput transcriptomics and comparative genomics
136 have produced very large sets of putative non-coding RNAs
137 and regulatory RNA signals. For many ofthem, evidence for
138 stabilizing selection acting on their secondary structures
139 has been derived, and at least approximate models of their
140 structures have been computed. The overwhelming majority of
141 these hypo-thetical RNAs cannot be assigned to established
142 families or classes. We present here a structure-based
143 clustering approach that is capable of extracting putative
144 RNA classesfrom genome-wide surveys for structured RNAs. The
145 LocARNA tool implements a novel variant of theSankoff
146 algorithm that is sufficiently fast to deal with several
147 thousand candidate sequences. The method is also robust
148 against false positive predictions, i.e., a contamination of
149 the input data with unstructured ornon-conserved
150 sequences. We have successfully tested the LocARNA-based
151 clustering approach on the sequences of the
152 RFAM-seedalignments. Furthermore, we have applied it to a
153 previously published set of 3332 predicted structured
154 elements in the Ciona intestinalis genomes (Missal et al.,
155 Bioinformatics 21(S2), i77-i78). In addition torecovering
156 e.g. tRNAs as a structure-based class, the method identifies
157 several RNA families, including microRNA and snoRNA
158 candidates, and suggests several novel classes of ncRNAs for
159 which to-date norepresentative has been experimentally
160 characterized.}
161 }
162
163 </citation>
164 <citation type="bibtex">@Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010,
165 author = {Smith, Cameron and Heyne, Steffen and Richter, Andreas S.
166 and Will, Sebastian and Backofen, Rolf},
167 title = {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA},
168 {ExpaRNA} and {LocARNA}},
169 journal = NAR,
170 year = {2010},
171 volume = {38 Suppl},
172 number = {},
173 pages = {W373-7},
174 user = {arichter},
175 pmid = {20444875},
176 doi = {10.1093/nar/gkq316},
177 issn = {0305-1048},
178 issn = {1362-4962},
179 abstract = {The Freiburg RNA tools web server integrates three tools
180 for the advanced analysis of RNA in a common web-based user
181 interface. The tools IntaRNA, ExpaRNA and LocARNA support
182 the prediction of RNA-RNA interaction, exact RNA matching
183 and alignment of RNA, respectively. The Freiburg RNA tools
184 web server and the software packages of the stand-alone
185 tools are freely accessible at
186 http://rna.informatik.uni-freiburg.de.}
187 }
188 </citation>
189 </citations>
190 </tool>