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Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.
author crs4
date Mon, 27 Oct 2014 06:45:52 -0400
parents 5c0030f52b83
children f5e44aad6498
comparison
equal deleted inserted replaced
5:b9fea998270a 6:3ad7ef0ba385
1 <tool id="prokka" name="Prokka" version="1.3.0"> 1 <tool id="prokka" name="Prokka" version="1.4.0">
2 <description>prokaryotic genome annotation</description> 2 <description>prokaryotic genome annotation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.2.28">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> 7 <requirement type="package" version="2.60">prodigal</requirement>
8 <requirement type="package" version="22.4">tbl2asn</requirement> 8 <requirement type="package" version="23.7">tbl2asn</requirement>
9 <requirement type="package" version="20131122">gnu_parallel</requirement> 9 <requirement type="package" version="20131122">gnu_parallel</requirement>
10 <requirement type="package" version="0.3">barrnap</requirement> 10 <requirement type="package" version="0.5">barrnap</requirement>
11 <requirement type="package" version="1.1">infernal</requirement> 11 <requirement type="package" version="1.1">infernal</requirement>
12 <requirement type="package" version="0.1.4">minced</requirement> 12 <requirement type="package" version="0.1.6">minced</requirement>
13 <requirement type="package" version="1.8">prokka</requirement> 13 <requirement type="package" version="1.10">prokka</requirement>
14 </requirements> 14 </requirements>
15 <version_command>prokka --version</version_command> 15 <version_command>prokka --version</version_command>
16 <command> 16 <command>
17 prokka 17 prokka
18 --cpus \${GALAXY_SLOTS:-8} 18 --cpus \${GALAXY_SLOTS:-8}
55 --gcode $kingdom.gcode 55 --gcode $kingdom.gcode
56 #end if 56 #end if
57 #if $usegenus 57 #if $usegenus
58 --usegenus 58 --usegenus
59 #end if 59 #end if
60 #if $proteins
61 --proteins $proteins
62 #end if
60 #if $metagenome 63 #if $metagenome
61 --metagenome 64 --metagenome
62 #end if 65 #end if
63 #if $fast 66 #if $fast
64 --fast 67 --fast
75 #if $notrna 78 #if $notrna
76 --notrna 79 --notrna
77 #end if 80 #end if
78 $input 81 $input
79 </command> 82 </command>
83 <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
84 <stdio>
85 <exit_code range="1:" />
86 </stdio>
80 <inputs> 87 <inputs>
81 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> 88 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
82 <param name="locustag" type="text" value="PROKKA" optional="true" label="Locus tag prefix (--locustag)" /> 89 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
83 <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)"> 90 <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)">
84 <validator type="in_range" min="1" /> 91 <validator type="in_range" min="1" />
85 </param> 92 </param>
86 <param name="gffver" type="select" label="GFF version (--gffver)"> 93 <param name="gffver" type="select" label="GFF version (--gffver)">
87 <option value="3">3</option> 94 <option value="3">3</option>
97 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" /> 104 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
98 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" /> 105 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
99 </when> 106 </when>
100 <when value="yes" /> 107 <when value="yes" />
101 </conditional> 108 </conditional>
102 <param name="centre" type="text" value="" optional="true" label="Sequencing centre ID (--centre)" /> 109 <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
103 <param name="genus" type="text" value="" optional="true" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" /> 110 <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
104 <param name="species" type="text" value="" optional="true" label="Species name (--species)" /> 111 <param name="species" type="text" value="" label="Species name (--species)" />
105 <param name="strain" type="text" value="" optional="true" label="Strain name (--strain)" /> 112 <param name="strain" type="text" value="" label="Strain name (--strain)" />
106 <param name="plasmid" type="text" value="" optional="true" label="Plasmid name or identifier (--plasmid)" /> 113 <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
107 <conditional name="kingdom"> 114 <conditional name="kingdom">
108 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)"> 115 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
109 <option value="Archaea">Archaea</option> 116 <option value="Archaea">Archaea</option>
110 <option value="Bacteria" selected="true">Bacteria</option> 117 <option value="Bacteria" selected="true">Bacteria</option>
111 <option value="Viruses">Viruses</option> 118 <option value="Viruses">Viruses</option>
124 <when value="Viruses"> 131 <when value="Viruses">
125 <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 --> 132 <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 -->
126 </when> 133 </when>
127 </conditional> 134 </conditional>
128 <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" /> 135 <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" />
136 <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
129 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" /> 137 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
130 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" /> 138 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
131 <param name="evalue" type="float" value="1e-06" optional="true" label="Similarity e-value cut-off"> 139 <param name="evalue" type="float" value="1e-06" optional="true" label="Similarity e-value cut-off">
132 <validator type="in_range" min="0" /> 140 <validator type="in_range" min="0" />
133 </param> 141 </param>
182 txt 190 txt
183 Statistics relating to the annotated features found 191 Statistics relating to the annotated features found
184 192
185 **License and citation** 193 **License and citation**
186 194
187 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_, Lionel Guy and is released under the `MIT license`_. 195 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_, © 2013 Lionel Guy and is released under the `MIT license`_.
188 196
189 .. _CRS4 Srl.: http://www.crs4.it/ 197 .. _CRS4 Srl.: http://www.crs4.it/
190 .. _MIT license: http://opensource.org/licenses/MIT 198 .. _MIT license: http://opensource.org/licenses/MIT
191 199
192 If you use this tool in Galaxy, please cite |Cuccuru2013|_. 200 You can use this tool only if you agree to the license terms of: `Prokka`_.
193
194 .. |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*
195 .. _Cuccuru2013: http://orione.crs4.it/
196
197 This tool uses `Prokka`_, which is licensed separately. Please cite Seemann, T. (2013) Prokka: Rapid Prokaryotic Genome Annotation. *Submitted*
198 201
199 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml 202 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
203
204 If you use this tool, please cite:
205
206 - |Cuccuru2014|_
207 - |Seemann2014|_.
208
209 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
210 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
211 .. |Seemann2014| replace:: Seemann, T. (2014) Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 30(14), 2068-2069
212 .. _Seemann2014: http://bioinformatics.oxfordjournals.org/content/30/14/2068
200 </help> 213 </help>
214 <citations>
215 <citation type="doi">10.1093/bioinformatics/btu135</citation>
216 <citation type="doi">10.1093/bioinformatics/btu153</citation>
217 </citations>
201 </tool> 218 </tool>