Mercurial > repos > iuc > bp_genbank2gff3

annotate bp_genbank2gff3.xml @ 0:f79bcd53b9a3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
author iuc
date Fri, 09 Oct 2015 09:19:49 -0400
parents
children 792a280ebeea
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
1 <tool id="bp_genbank2gff3" name="Genbank to GFF3" version="1.0">
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
2 <description>converter</description>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
3 <macros>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
4 <import>macros.xml</import>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
5 </macros>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
6 <expand macro="stdio" />
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
7 <command><![CDATA[
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
8 bp_genbank2gff3.pl
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
9 $noinfer
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
10 #if str($sofile.sofile) != "__none__":
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
11 --sofile
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
12 #if str($sofile.sofile) == "url":
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
13 "${sofile.so_url}"
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
14 #else:
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
15 live
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
16 #end if
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
17 #end if
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
18 --outdir -
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
19 --ethresh $ethresh
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
20 $model
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
21 --typesource "${typesource}"
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
22
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
23 $genbank
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
24 > $gff3]]></command>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
25 <inputs>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
26 <param label="Genbank file" name="genbank" type="data" format="gb"/>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
27 <param name="noinfer" truevalue="" falsevalue="--noinfer" checked="true" type="boolean" label="Infer exon/mRNA subfeatures"/>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
28 <conditional name="sofile" label="Sequence Ontology">
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
29 <param name="sofile" label="Sequence Ontology File" type="select">
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
30 <option value="__none__" selected="True">None specified</option>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
31 <option value="live">Latest Sequence Ontology</option>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
32 <option value="url">User Specified</option>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
33 </param>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
34 <when value="__none__" />
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
35 <when value="live" />
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
36 <when value="url">
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
37 <param name="so_url" label="Sequence Ontology URL" type="text"/>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
38 </when>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
39 </conditional>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
40 <param name="ethresh" label="Error threshold for unflattener" type="select">
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
41 <option value="0">Strict</option>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
42 <option value="1" selected="True">Medium</option>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
43 <option value="2">Loose</option>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
44 <option value="3">Ignore Errors</option>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
45 </param>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
46 <param name="model" label="Gene Model" type="select">
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
47 <option value="--CDS" selected="True">Default GFF gene model</option>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
48 <option value="--noCDS">Alternate gene-RNA-protein-exon model</option>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
49 </param>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
50 <param name="typesource" label="Sequence Ontology type for landmark feature" help="E.g. chromosome, region, contig" value="contig" type="text" />
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
51 </inputs>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
52 <outputs>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
53 <data format="gff3" name="gff3" label="${genbank.name} as GFF3"/>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
54 </outputs>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
55 <tests>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
56 <test>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
57 <param name="genbank" value="seq.gb" />
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
58 <param name="noinfer" value="True" />
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
59 <output name="gff3" file="seq.gb.0.gff" ftype="gff3" lines_diff="6"/>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
60 </test>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
61 <test>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
62 <param name="genbank" value="seq.gb" />
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
63 <output name="gff3" file="seq.gb.1.gff" ftype="gff3" lines_diff="4"/>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
64 </test>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
65 </tests>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
66 <help><![CDATA[
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
67 **What it does**:
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
68
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
69 This tool uses Bio::SeqFeature::Tools::Unflattener and
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
70 Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with gene
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
71 containment hierarchies mapped for optimal display in gbrowse.
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
72
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
73 The input files are assumed to be gzipped GenBank flatfiles for refseq
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
74 contigs. The files may contain multiple GenBank records.
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
75
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
76 **Designed for RefSeq**
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
77
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
78 This script is designed for RefSeq genomic sequence entries. It may
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
79 work for third party annotations but this has not been tested.
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
80 But see below, Uniprot/Swissprot works, EMBL and possibly EMBL/Ensembl
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
81 if you don't mind some gene model unflattener errors (dgg).
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
82
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
83 **G-R-P-E Gene Model**
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
84
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
85 Don Gilbert worked this over with needs to produce GFF3 suited to
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
86 loading to GMOD Chado databases.
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
87
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
88 This writes GFF with an alternate, but useful Gene model,
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
89 instead of the consensus model for GFF3
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
90
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
91 [ gene > mRNA> (exon,CDS,UTR) ]
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
92
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
93 This alternate is
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
94
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
95 gene > mRNA > polypeptide > exon
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
96
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
97 means the only feature with dna bases is the exon. The others
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
98 specify only location ranges on a genome. Exon of course is a child
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
99 of mRNA and protein/peptide.
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
100
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
101 The protein/polypeptide feature is an important one, having all the
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
102 annotations of the GenBank CDS feature, protein ID, translation, GO
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
103 terms, Dbxrefs to other proteins.
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
104
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
105 UTRs, introns, CDS-exons are all inferred from the primary exon bases
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
106 inside/outside appropriate higher feature ranges. Other special gene
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
107 model features remain the same.
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
108
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
109 **Authors**
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
110
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
111 Sheldon McKay (mckays@cshl.edu)
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
112
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
113 Copyright (c) 2004 Cold Spring Harbor Laboratory.
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
114
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
115 **Author of hacks for GFF2Chado loading**
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
116
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
117 Don Gilbert (gilbertd@indiana.edu)
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
118 ]]></help>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
119 <citations>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
120 <citation type="doi">10.1101/gr.361602</citation>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
121 </citations>
f79bcd53b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl commit 799339e22181d28cb2b145454d353d6025779636
iuc
parents:
diff changeset
122 </tool>