annotate rnammer.xml @ 35:fa736576c7ed draft

planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
author jjkoehorst
date Mon, 04 Jul 2016 10:37:59 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
35
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
1 <tool id="DRnammer" name="rRNA detection" version="1.0.0">
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
2 <description/>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
3 <requirements>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
4 <container type="docker">jjkoehorst/sappdocker:RNAMMER</container>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
5 </requirements>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
6 <command interpreter="docker">java -jar /rnammer/rnammer-0.0.1-SNAPSHOT-jar-with-dependencies.jar
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
7 '-input' '$input' -output '$output' -format TURTLE
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
8 </command>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
9 <inputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
10 <param format="ttl" label="genome ttl file" name="input" type="data"/>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
11 </inputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
12 <outputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
13 <data format="ttl" label="RNA: ${input.name}" name="output"/>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
14 </outputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
15 <help>Be aware that this can only be used for academic users; other
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
16 users are
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
17 requested to contact CBS Software Package Manager at
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
18 software@cbs.dtu.dk.
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
19 We are investigating alternative prediction
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
20 applications, please contact
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
21 us if you are aware of such method.
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
22 </help>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
23 <citations>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
24 <citation type="bibtex">@article{Lagesen2007,
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
25 abstract = {The
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
26 publication of a complete genome sequence is usually
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
27 accompanied by
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
28 annotations of its genes. In contrast to protein
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
29 coding genes, genes
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
30 for ribosomal RNA (rRNA) are often poorly or
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
31 inconsistently annotated.
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
32 This makes comparative studies based on
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
33 rRNA genes difficult. We have
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
34 therefore created computational
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
35 predictors for the major rRNA species
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
36 from all kingdoms of life and
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
37 compiled them into a program called
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
38 RNAmmer. The program uses hidden
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
39 Markov models trained on data from
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
40 the 5S ribosomal RNA database and
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
41 the European ribosomal RNA database
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
42 project. A pre-screening step
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
43 makes the method fast with little loss
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
44 of sensitivity, enabling the
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
45 analysis of a complete bacterial genome
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
46 in less than a minute.
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
47 Results from running RNAmmer on a large set of
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
48 genomes indicate that
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
49 the location of rRNAs can be predicted with a
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
50 very high level of
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
51 accuracy. Novel, unannotated rRNAs are also
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
52 predicted in many
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
53 genomes. The software as well as the genome analysis
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
54 results are
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
55 available at the CBS web server.},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
56 author = {Lagesen, Karin
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
57 and Hallin, Peter and R\o dland, Einar Andreas and
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
58 Staerfeldt,
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
59 Hans-Henrik and Rognes, Torbj\o rn and Ussery, David W},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
60 doi =
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
61 {10.1093/nar/gkm160},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
62 file = {:Users/koeho006/Library/Application
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
63 Support/Mendeley
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
64 Desktop/Downloaded/Lagesen et al. - 2007 - RNAmmer
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
65 consistent and
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
66 rapid annotation of ribosomal RNA genes.pdf:pdf},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
67 issn =
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
68 {1362-4962},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
69 journal = {Nucleic acids research},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
70 keywords =
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
71 {Computational Biology,Computational Biology: methods,Genes,
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
72 rRNA,Genome, Bacterial,Genomics,Genomics: methods,Markov
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
73 Chains,Software},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
74 mendeley-groups = {Dump/VAPP Paper,VAPP Application
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
75 note},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
76 month = jan,
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
77 number = {9},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
78 pages = {3100--8},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
79 pmid = {17452365},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
80 title = {{RNAmmer: consistent and rapid annotation of ribosomal RNA
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
81 genes.}},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
82 volume = {35},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
83 year = {2007}
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
84 }
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
85 </citation>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
86 </citations>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
87 </tool>