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Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
author crs4
date Fri, 25 Oct 2013 08:59:51 -0400
parents 4b6f16a79fe4
children fffa1ae330ae
comparison
equal deleted inserted replaced
1:4b6f16a79fe4 2:4bafaa074484
1 <tool id="prokka" name="Prokka" version="1.0.1"> 1 <tool id="prokka" name="Prokka" version="1.1.0">
2 <description>Prokaryotic Annotation</description> 2 <description>prokaryotic genome annotation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.2.26+">blast+</requirement> 4 <requirement type="package" version="2.2.28">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>
7 <requirement type="package" version="2.60">prodigal</requirement>
8 <requirement type="binary">tbl2asn</requirement>
9 <requirement type="binary">parallel</requirement>
10 <requirement type="package" version="0.2">barrnap</requirement>
7 <requirement type="package" version="1.1rc4">infernal</requirement> 11 <requirement type="package" version="1.1rc4">infernal</requirement>
8 <requirement type="package" version="1.7">prokka</requirement> 12 <requirement type="package" version="1.7">prokka</requirement>
9 </requirements> 13 </requirements>
10 <version_command>prokka --version</version_command> 14 <version_command>prokka --version</version_command>
11 <command interpreter="python"> 15 <command>
12 prokka.py 16 prokka
13 \${PROKKA_SITE_OPTIONS:---cpus 8} 17 \${PROKKA_SITE_OPTIONS:---cpus 8}
14 ## Reads in FASTA format 18 --quiet ## to avoid non-error messages written to stderr
15 --fasta=$fasta_file 19 --outdir outdir --prefix prokka ## used in outputs section
16 ## Additional inputs 20 #if $locustag
17 --kingdom $kingdom_type.kingdom 21 --locustag "$locustag"
18 #if str($mincontig) 22 #end if
19 --mincontig $mincontig 23 #if str($increment)
24 --increment $increment
25 #end if
26 --gffver $gffver
27 #if $compliant.compliant_select == "no"
28 #if $compliant.addgenes
29 --addgenes
30 #end if
31 #if str($compliant.mincontig)
32 --mincontig $compliant.mincontig
33 #end if
34 #else
35 --compliant
36 #end if
37 #if $centre
38 --centre "$centre"
39 #end if
40 #if $genus
41 --genus "$genus"
42 #end if
43 #if $species
44 --species "$species"
45 #end if
46 #if $strain
47 --strain "$strain"
48 #end if
49 #if $plasmid
50 --plasmid "$plasmid"
51 #end if
52 --kingdom $kingdom.kingdom_select
53 #if str($kingdom.gcode)
54 --gcode $kingdom.gcode
55 #end if
56 #if $usegenus
57 --usegenus
58 #end if
59 #if $metagenome
60 --metagenome
61 #end if
62 #if $fast
63 --fast
64 #end if
65 #if str($evalue)
66 --evalue $evalue
20 #end if 67 #end if
21 #if $rfam 68 #if $rfam
22 --rfam 69 --rfam
23 #end if 70 #end if
24 #if $centre 71 #if $norrna
25 --centre "$centre" 72 --norrna
26 #end if 73 #end if
27 ## Output files 74 #if $notrna
28 --gff=$out_gff 75 --notrna
29 --gbk=$out_gbk 76 #end if
30 --fna=$out_fna 77 $input
31 --faa=$out_faa
32 --ffn=$out_ffn
33 --sqn=$out_sqn
34 --fsa=$out_fsa
35 --tbl=$out_tbl
36 --err=$out_err
37 --txt=$out_txt
38 --log=$out_log
39 </command> 78 </command>
40 <inputs> 79 <inputs>
41 <param name="fasta_file" type="data" format="fasta" label="Contigs" help="FASTA format" /> 80 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
42 <conditional name="kingdom_type"> 81 <param name="locustag" type="text" value="PROKKA" optional="true" label="Locus tag prefix (--locustag)" />
43 <param name="kingdom" type="select" label="Kingdom (--kingdom)"> 82 <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)">
83 <validator type="in_range" min="1" />
84 </param>
85 <param name="gffver" type="select" label="GFF version (--gffver)">
86 <option value="3">3</option>
87 <option value="2">2</option>
88 <option value="1">1</option>
89 </param>
90 <conditional name="compliant">
91 <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance (--compliant)" help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below)">
92 <option value="no">No</option>
93 <option value="yes">Yes</option>
94 </param>
95 <when value="no">
96 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
97 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
98 </when>
99 <when value="yes" />
100 </conditional>
101 <param name="centre" type="text" value="" optional="true" label="Sequencing centre ID (--centre)" />
102 <param name="genus" type="text" value="" optional="true" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
103 <param name="species" type="text" value="" optional="true" label="Species name (--species)" />
104 <param name="strain" type="text" value="" optional="true" label="Strain name (--strain)" />
105 <param name="plasmid" type="text" value="" optional="true" label="Plasmid name or identifier (--plasmid)" />
106 <conditional name="kingdom">
107 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
44 <option value="Archaea">Archaea</option> 108 <option value="Archaea">Archaea</option>
45 <option value="Bacteria" selected="true">Bacteria</option> 109 <option value="Bacteria" selected="true">Bacteria</option>
46 <option value="Viruses">Viruses</option> 110 <option value="Viruses">Viruses</option>
47 </param> 111 </param>
48 <when value="Archaea" /> 112 <when value="Archaea">
49 <when value="Bacteria" /> 113 <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
50 <when value="Viruses" /> 114 </when>
115 <when value="Bacteria">
116 <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
117 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
118 <option selected="true" value="none">N/A</option>
119 <option value="pos">positive</option>
120 <option value="neg">negative</option>
121 </param> SignalP is not FOSS -->
122 </when>
123 <when value="Viruses">
124 <param name="gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
125 </when>
51 </conditional> 126 </conditional>
52 <param name="mincontig" type="integer" value="200" optional="true" label="Minimun contig size - NCBI needs 200 (--mincontig)" /> 127 <param name="usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database (--usegenus)" help="Will use the BLAST database for the genus specified above, if installed" />
53 <param name="centre" type="text" value="CRS4" label="Sequencing centre ID (--centre)" /> 128 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
54 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal-Rfam - SLOW (--rfam)" /> 129 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
130 <param name="evalue" type="float" value="1e-06" optional="true" label="Similarity e-value cut-off">
131 <validator type="in_range" min="0" />
132 </param>
133 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
134 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
135 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
55 </inputs> 136 </inputs>
56 <outputs> 137 <outputs>
57 <data format="gff" name="out_gff" label="${tool.name} on ${on_string}: gff" /> 138 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff" />
58 <data format="txt" name="out_gbk" label="${tool.name} on ${on_string}: gbk" /> 139 <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk" />
59 <data format="fasta" name="out_fna" label="${tool.name} on ${on_string}: fna" /> 140 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna" />
60 <data format="fasta" name="out_faa" label="${tool.name} on ${on_string}: faa" /> 141 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa" />
61 <data format="fasta" name="out_ffn" label="${tool.name} on ${on_string}: ffn" /> 142 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn" />
62 <data format="asn1" name="out_sqn" label="${tool.name} on ${on_string}: sqn" /> 143 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn" />
63 <data format="fasta" name="out_fsa" label="${tool.name} on ${on_string}: fsa" /> 144 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa" />
64 <data format="txt" name="out_tbl" label="${tool.name} on ${on_string}: tbl" /> 145 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl" />
65 <data format="txt" name="out_err" label="${tool.name} on ${on_string}: err" /> 146 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err" />
66 <data format="txt" name="out_txt" label="${tool.name} on ${on_string}: txt" /> 147 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt" />
67 <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log" /> 148 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
68 </outputs> 149 </outputs>
69
70 <help> 150 <help>
71 **What it does** 151 **What it does**
72 152
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. 153 Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.
74 154
75 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml 155 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
76 156
77 **Output files** 157 **Output files**
78 158
79 Prokka creates several output files: 159 Prokka creates several output files:
80 160
81 gff 161 gff
82 This is the master annotation in GFF3 format, containing both sequences and annotations 162 This is the master annotation in GFF format, containing both sequences and annotations
83 gbk 163 gbk
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 164 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
85 fna 165 fna
86 Nucleotide FASTA file of the input contig sequences 166 Nucleotide FASTA file of the input contig sequences
87 faa 167 faa
101 txt 181 txt
102 Statistics relating to the annotated features found 182 Statistics relating to the annotated features found
103 183
104 **License and citation** 184 **License and citation**
105 185
106 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. 186 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_, Lionel Guy and is released under the `MIT license`_.
107 187
108 .. _CRS4 Srl.: http://www.crs4.it/ 188 .. _CRS4 Srl.: http://www.crs4.it/
109 .. _MIT license: http://opensource.org/licenses/MIT 189 .. _MIT license: http://opensource.org/licenses/MIT
110 190
111 If you use this tool in Galaxy, please cite |Cuccuru2013|_. 191 If you use this tool in Galaxy, please cite |Cuccuru2013|_.