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comparison bp_genbank2gff3.xml @ 0:f79bcd53b9a3 draft

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