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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
author iuc
date Fri, 28 Oct 2016 12:37:17 -0400
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1 <tool id="prokka" name="Prokka" version="1.11.1">
2 <description>prokaryotic genome annotation</description>
3 <requirements>
4 <requirement type="package" version="1.11">prokka</requirement>
5 </requirements>
6 <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
7 <stdio>
8 <exit_code range="1:" />
9 </stdio>
10 <version_command>prokka --version</version_command>
11 <command><![CDATA[
12 prokka
13 --cpus \${GALAXY_SLOTS:-8}
14 --quiet ## to avoid non-error messages written to stderr
15 --outdir outdir --prefix prokka ## used in outputs section
16 #if $locustag
17 --locustag '$locustag'
18 #end if
19 #if str($increment)
20 --increment $increment
21 #end if
22 --gffver $gffver
23 #if $compliant.compliant_select == "no"
24 #if $compliant.addgenes
25 --addgenes
26 #end if
27 #if str($compliant.mincontig)
28 --mincontig $compliant.mincontig
29 #end if
30 #else
31 --compliant
32 #end if
33 #if $centre
34 --centre '$centre'
35 #end if
36 #if $genus
37 --genus '$genus'
38 #end if
39 #if $species
40 --species '$species'
41 #end if
42 #if $strain
43 --strain '$strain'
44 #end if
45 #if $plasmid
46 --plasmid '$plasmid'
47 #end if
48 --kingdom $kingdom.kingdom_select
49 #if str($kingdom.gcode)
50 --gcode $kingdom.gcode
51 #end if
52 #if $usegenus
53 --usegenus
54 #end if
55 #if $proteins
56 --proteins '$proteins'
57 #end if
58 #if $metagenome
59 --metagenome
60 #end if
61 #if $fast
62 --fast
63 #end if
64 #if str($evalue)
65 --evalue $evalue
66 #end if
67 #if $rfam
68 --rfam
69 #end if
70 #if $norrna
71 --norrna
72 #end if
73 #if $notrna
74 --notrna
75 #end if
76 $input
77 ]]></command>
78 <inputs>
79 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
80 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
81 <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" />
82 <param name="gffver" type="select" label="GFF version (--gffver)">
83 <option value="3">3</option>
84 <option value="2">2</option>
85 <option value="1">1</option>
86 </param>
87 <conditional name="compliant">
88 <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)">
89 <option value="no">No</option>
90 <option value="yes">Yes</option>
91 </param>
92 <when value="no">
93 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
94 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
95 </when>
96 <when value="yes" />
97 </conditional>
98 <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
99 <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
100 <param name="species" type="text" value="" label="Species name (--species)" />
101 <param name="strain" type="text" value="" label="Strain name (--strain)" />
102 <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
103 <conditional name="kingdom">
104 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
105 <option value="Archaea">Archaea</option>
106 <option value="Bacteria" selected="true">Bacteria</option>
107 <option value="Viruses">Viruses</option>
108 </param>
109 <when value="Archaea">
110 <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 -->
111 </when>
112 <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 -->
114 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
115 <option selected="true" value="none">N/A</option>
116 <option value="pos">positive</option>
117 <option value="neg">negative</option>
118 </param> SignalP is not FOSS -->
119 </when>
120 <when value="Viruses">
121 <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 -->
122 </when>
123 </conditional>
124 <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" />
125 <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
126 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
127 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
128 <param name="evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
129 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
130 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
131 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
132
133 <param name="outputs" type="select" multiple="true" label="Additional outputs">
134 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations</option>
135 <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence</option>
136 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences</option>
137 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences</option>
138 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS</option>
139 <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.</option>
140 <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines</option>
141 <option value="tbl" selected="True">Feature Table file</option>
142 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report</option>
143 <option value="txt" selected="True">Statistics relating to the annotated features found</option>
144 </param>
145
146 </inputs>
147 <outputs>
148 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
149 <filter>'gff' in outputs</filter>
150 </data>
151 <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
152 <filter>'gbk' in outputs</filter>
153 </data>
154 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
155 <filter>'fna' in outputs</filter>
156 </data>
157 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
158 <filter>'faa' in outputs</filter>
159 </data>
160 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
161 <filter>'ffn' in outputs</filter>
162 </data>
163 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
164 <filter>'sqn' in outputs</filter>
165 </data>
166 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
167 <filter>'fsa' in outputs</filter>
168 </data>
169 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
170 <filter>'tbl' in outputs</filter>
171 </data>
172 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
173 <filter>'err' in outputs</filter>
174 </data>
175 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
176 <filter>'txt' in outputs</filter>
177 </data>
178 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
179 </outputs>
180 <tests>
181 <test>
182 <param name="input" ftype="fasta" value="phiX174.fasta" />
183 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" />
184 <output name="out_gff" file="out.gff" />
185 <output name="out_gbk" file="out.gbk" lines_diff="14" />
186 <output name="out_fna" file="out.fna" />
187 <output name="out_faa" file="out.faa" />
188 <output name="out_ffn" file="out.ffn" />
189 <output name="out_sqn" file="out.sqn" lines_diff="84" />
190 <output name="out_fsa" file="out.fsa" />
191 <output name="out_tbl" file="out.tbl" />
192 <output name="out.err" file="out.err" />
193 <output name="out_txt" file="out.txt" />
194 <output name="out_log">
195 <assert_contents>
196 <has_text text="Type 'prokka --citation' for more details." />
197 </assert_contents>
198 </output>
199 </test>
200 </tests>
201 <help><![CDATA[
202 **What it does**
203
204 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.
205
206 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
207
208 **Output files**
209
210 Prokka creates several output files:
211
212 gff
213 This is the master annotation in GFF format, containing both sequences and annotations
214 gbk
215 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
216 fna
217 Nucleotide FASTA file of the input contig sequences
218 faa
219 Protein FASTA file of the translated CDS sequences
220 ffn
221 Nucleotide FASTA file of all the annotated sequences, not just CDS
222 sqn
223 An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.
224 fsa
225 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
226 tbl
227 Feature Table file, used by "tbl2asn" to create the .sqn file
228 err
229 Unacceptable annotations - the NCBI discrepancy report
230 log
231 Contains all the output that Prokka produced during its run
232 txt
233 Statistics relating to the annotated features found
234
235 **License and citation**
236
237 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
238
239 .. _CRS4 Srl.: http://www.crs4.it/
240 .. _Earlham Institute: http://earlham.ac.uk/
241 .. _MIT license: https://opensource.org/licenses/MIT
242
243 You can use this tool only if you agree to the license terms of: `Prokka`_.
244
245 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
246 ]]></help>
247 <citations>
248 <citation type="doi">10.1093/bioinformatics/btu135</citation>
249 <citation type="doi">10.1093/bioinformatics/btu153</citation>
250 </citations>
251 </tool>