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comparison prokka.xml @ 0:95505a9fa26f draft

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author crs4
date Tue, 10 Sep 2013 13:11:26 -0400
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1 <tool id="prokka" name="Prokka" version="1.0.0">
2 <description>Prokaryotic Annotation</description>
3 <requirements>
4 <requirement type="package" version="2.2.26+">blast+</requirement>
5 <requirement type="package" version="3.1b1">hmmer</requirement>
6 <requirement type="package" version="1.2.36">aragorn</requirement>
7 <requirement type="package" version="1.1rc4">infernal</requirement>
8 <requirement type="package" version="1.7">prokka</requirement>
9 </requirements>
10 <version_command>prokka --version</version_command>
11 <command interpreter="python">
12 prokka.py
13 \${PROKKA_SITE_OPTIONS:---cpus 8}
14 ## Reads in FASTA format
15 --fasta=$fasta_file
16 ## Additional inputs
17 --kingdom $kingdom_type.kingdom
18 #if str($mincontig)
19 --mincontig $mincontig
20 #end if
21 #if $rfam
22 --rfam
23 #end if
24 #if $centre
25 --centre "$centre"
26 #end if
27 ## Output files
28 --gff=$out_gff
29 --gbk=$out_gbk
30 --fna=$out_fna
31 --faa=$out_faa
32 --ffn=$out_ffn
33 --sqn=$out_sqn
34 --fsa=$out_fsa
35 --tbl=$out_tbl
36 --err=$out_err
37 --log=$out_log
38 </command>
39 <inputs>
40 <param name="fasta_file" type="data" format="fasta" label="Contigs" help="FASTA format" />
41 <conditional name="kingdom_type">
42 <param name="kingdom" type="select" label="Kingdom (--kingdom)">
43 <option value="Archaea">Archaea</option>
44 <option value="Bacteria" selected="true">Bacteria</option>
45 <option value="Viruses">Viruses</option>
46 </param>
47 <when value="Archaea" />
48 <when value="Bacteria" />
49 <when value="Viruses" />
50 </conditional>
51 <param name="mincontig" type="integer" value="200" optional="true" label="Minimun contig size - NCBI needs 200 (--mincontig)" />
52 <param name="centre" type="text" value="CRS4" label="Sequencing centre ID (--centre)" />
53 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal-Rfam - SLOW (--rfam)" />
54 </inputs>
55 <outputs>
56 <data format="gff" name="out_gff" label="${tool.name} on ${on_string}: gff"/>
57 <data format="txt" name="out_gbk" label="${tool.name} on ${on_string}: gbk"/>
58 <data format="fasta" name="out_fna" label="${tool.name} on ${on_string}: fna"/>
59 <data format="fasta" name="out_faa" label="${tool.name} on ${on_string}: faa"/>
60 <data format="fasta" name="out_ffn" label="${tool.name} on ${on_string}: ffn"/>
61 <data format="asn1" name="out_sqn" label="${tool.name} on ${on_string}: sqn"/>
62 <data format="fasta" name="out_fsa" label="${tool.name} on ${on_string}: fsa"/>
63 <data format="txt" name="out_tbl" label="${tool.name} on ${on_string}: tbl"/>
64 <data format="txt" name="out_err" label="${tool.name} on ${on_string}: err"/>
65 <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log"/>
66 </outputs>
67
68 <help>
69 **What it does**
70
71 Prokka_ is a software tool to annotate bacterial, archaeal and viral genomes very rapidly, and produce output files that require only minor tweaking to submit to Genbank/ENA/DDBJ.
72
73 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
74
75 **Output files**
76
77 Prokka creates several output files::
78
79 gff This is the master annotation in GFF3 format, containing both sequences and annotations.
80 It can be viewed directly in Artemis or IGV
81 gbk This is a standard Genbank file derived from the master .gff
82 If the input to prokka was a multi-FASTA, then this will be a multi-Genbank,
83 with one record for each sequence
84 fna Nucleotide FASTA file of the input contig sequences
85 faa Protein FASTA file of the translated CDS sequences
86 ffn Nucleotide FASTA file of all the annotated sequences, not just CDS
87 sqn An ASN1 format "Sequin" file for submission to Genbank.
88 It needs to be edited to set the correct taxonomy, authors, related publication etc.
89 fsa Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file.
90 It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines
91 tbl Feature Table file, used by "tbl2asn" to create the .sqn file.
92 err Unacceptable annotations - the NCBI discrepancy report.
93 log Contains all the output that Prokka produced during its run.
94 This is a record of what settings you used.
95
96 **License and citation**
97
98 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
99
100 .. _CRS4 Srl.: http://www.crs4.it/
101 .. _MIT license: http://opensource.org/licenses/MIT
102
103 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
104
105 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
106 .. _Cuccuru2013: http://orione.crs4.it/
107
108 This tool uses `Prokka`_, which is licensed separately. Please cite Seemann T. Prokka: Prokaryotic Genome Annotation System (in preparation).
109
110 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
111 </help>
112 </tool>