Mercurial > repos > crs4 > prokka

comparison prokka.xml @ 1:4b6f16a79fe4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add txt output file. Use a definition list instead of a block quote in <help>. Correct 2 dependency minimum versions.
author crs4
date Thu, 26 Sep 2013 12:39:52 -0400
parents 95505a9fa26f
children 4bafaa074484
comparison
equal deleted inserted replaced
0:95505a9fa26f 1:4b6f16a79fe4
1 <tool id="prokka" name="Prokka" version="1.0.0"> 1 <tool id="prokka" name="Prokka" version="1.0.1">
2 <description>Prokaryotic Annotation</description> 2 <description>Prokaryotic Annotation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.2.26+">blast+</requirement> 4 <requirement type="package" version="2.2.26+">blast+</requirement>
5 <requirement type="package" version="3.1b1">hmmer</requirement> 5 <requirement type="package" version="3.1b1">hmmer</requirement>
6 <requirement type="package" version="1.2.36">aragorn</requirement> 6 <requirement type="package" version="1.2.36">aragorn</requirement>
32 --ffn=$out_ffn 32 --ffn=$out_ffn
33 --sqn=$out_sqn 33 --sqn=$out_sqn
34 --fsa=$out_fsa 34 --fsa=$out_fsa
35 --tbl=$out_tbl 35 --tbl=$out_tbl
36 --err=$out_err 36 --err=$out_err
37 --txt=$out_txt
37 --log=$out_log 38 --log=$out_log
38 </command> 39 </command>
39 <inputs> 40 <inputs>
40 <param name="fasta_file" type="data" format="fasta" label="Contigs" help="FASTA format" /> 41 <param name="fasta_file" type="data" format="fasta" label="Contigs" help="FASTA format" />
41 <conditional name="kingdom_type"> 42 <conditional name="kingdom_type">
51 <param name="mincontig" type="integer" value="200" optional="true" label="Minimun contig size - NCBI needs 200 (--mincontig)" /> 52 <param name="mincontig" type="integer" value="200" optional="true" label="Minimun contig size - NCBI needs 200 (--mincontig)" />
52 <param name="centre" type="text" value="CRS4" label="Sequencing centre ID (--centre)" /> 53 <param name="centre" type="text" value="CRS4" label="Sequencing centre ID (--centre)" />
53 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal-Rfam - SLOW (--rfam)" /> 54 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal-Rfam - SLOW (--rfam)" />
54 </inputs> 55 </inputs>
55 <outputs> 56 <outputs>
56 <data format="gff" name="out_gff" label="${tool.name} on ${on_string}: gff"/> 57 <data format="gff" name="out_gff" label="${tool.name} on ${on_string}: gff" />
57 <data format="txt" name="out_gbk" label="${tool.name} on ${on_string}: gbk"/> 58 <data format="txt" name="out_gbk" label="${tool.name} on ${on_string}: gbk" />
58 <data format="fasta" name="out_fna" label="${tool.name} on ${on_string}: fna"/> 59 <data format="fasta" name="out_fna" label="${tool.name} on ${on_string}: fna" />
59 <data format="fasta" name="out_faa" label="${tool.name} on ${on_string}: faa"/> 60 <data format="fasta" name="out_faa" label="${tool.name} on ${on_string}: faa" />
60 <data format="fasta" name="out_ffn" label="${tool.name} on ${on_string}: ffn"/> 61 <data format="fasta" name="out_ffn" label="${tool.name} on ${on_string}: ffn" />
61 <data format="asn1" name="out_sqn" label="${tool.name} on ${on_string}: sqn"/> 62 <data format="asn1" name="out_sqn" label="${tool.name} on ${on_string}: sqn" />
62 <data format="fasta" name="out_fsa" label="${tool.name} on ${on_string}: fsa"/> 63 <data format="fasta" name="out_fsa" label="${tool.name} on ${on_string}: fsa" />
63 <data format="txt" name="out_tbl" label="${tool.name} on ${on_string}: tbl"/> 64 <data format="txt" name="out_tbl" label="${tool.name} on ${on_string}: tbl" />
64 <data format="txt" name="out_err" label="${tool.name} on ${on_string}: err"/> 65 <data format="txt" name="out_err" label="${tool.name} on ${on_string}: err" />
65 <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log"/> 66 <data format="txt" name="out_txt" label="${tool.name} on ${on_string}: txt" />
67 <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log" />
66 </outputs> 68 </outputs>
67 69
68 <help> 70 <help>
69 **What it does** 71 **What it does**
70 72
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. 73 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 74
73 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml 75 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
74 76
75 **Output files** 77 **Output files**
76 78
77 Prokka creates several output files:: 79 Prokka creates several output files:
78 80
79 gff This is the master annotation in GFF3 format, containing both sequences and annotations. 81 gff
80 It can be viewed directly in Artemis or IGV 82 This is the master annotation in GFF3 format, containing both sequences and annotations
81 gbk This is a standard Genbank file derived from the master .gff 83 gbk
82 If the input to prokka was a multi-FASTA, then this will be a multi-Genbank, 84 This is a standard GenBank file derived from the master .gff . If the input to prokka was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence
83 with one record for each sequence 85 fna
84 fna Nucleotide FASTA file of the input contig sequences 86 Nucleotide FASTA file of the input contig sequences
85 faa Protein FASTA file of the translated CDS sequences 87 faa
86 ffn Nucleotide FASTA file of all the annotated sequences, not just CDS 88 Protein FASTA file of the translated CDS sequences
87 sqn An ASN1 format "Sequin" file for submission to Genbank. 89 ffn
88 It needs to be edited to set the correct taxonomy, authors, related publication etc. 90 Nucleotide FASTA file of all the annotated sequences, not just CDS
89 fsa Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. 91 sqn
90 It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines 92 An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.
91 tbl Feature Table file, used by "tbl2asn" to create the .sqn file. 93 fsa
92 err Unacceptable annotations - the NCBI discrepancy report. 94 Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines
93 log Contains all the output that Prokka produced during its run. 95 tbl
94 This is a record of what settings you used. 96 Feature Table file, used by "tbl2asn" to create the .sqn file
97 err
98 Unacceptable annotations - the NCBI discrepancy report
99 log
100 Contains all the output that Prokka produced during its run
101 txt
102 Statistics relating to the annotated features found
95 103
96 **License and citation** 104 **License and citation**
97 105
98 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. 106 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
99 107