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1 <tool id="prokka" name="prokka" version="0.1">
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2 <description>prokaryotic genome annotation</description>
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3 <requirements>
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4 <requirement type="package" version="1.6">prokka</requirement>
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5 <requirement type="package" version="1.2.36">aragorn</requirement>
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6 <requirement type="package" version="1.2">rnammer</requirement>
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7 <requirement type="package" version="2.60">prodigal</requirement>
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8 <requirement type="package" version="4.1">signalp</requirement>
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9 <requirement type="package" version="3.0">infernal</requirement>
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10 <requirement type="package" version="3.1">hmmer</requirement>
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11 <requirement type="package">blast+</requirement>
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12 <requirement type="package">tbl2asn</requirement>
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13 </requirements>
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14 <version_command>prokka --version</version_command>
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15 <command>prokka --outdir outdir --force
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16 --quiet ## To avoid messages written to stderr and causing galaxy errors
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17 --prefix prokka
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18 $addgenes
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19 --locustag $locustag
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20 --increment $increment
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21 --centre $centre
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22 --genus $genus --species $species --strain $strain
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23 --kingdom $kingdom
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24 --gcode $gcode
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25 #if $gram != "none"
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26 --gram $gram
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27 #end if
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28 $usegenus
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29 $metagenome
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30 $fast
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31 --cpus $cpus
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32 --mincontig $mincontig
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33 --evalue $evalue
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34 $input
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35 </command>
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36 <inputs>
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37 <param name="input" type="data" format="fasta" label="Contigs to annotate" />
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38 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix"/>
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39 <param name="addgenes" type="boolean" truevalue="--addgenes" falsevalue="" checked="false" label="Add 'gene' features for each 'CDS' feature" />
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40 <param name="increment" type="integer" value="10" label="Locus tag counter increment" />
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41 <param name="centre" type="text" value="molevoUU" label="Locus tag prefix"/>
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42 <param name="genus" type="text" value="Genus" label="Genus name (will be used to aid annotation)"/>
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43 <param name="species" type="text" value="species" label="Species name"/>
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44 <param name="strain" type="text" value="strain" label="Strain name"/>
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45 <param name="kingdom" type="select" display="radio" label="Annotation mode">
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46 <option value="Archaea">Archaea</option>
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47 <option value="Bacteria" selected="True">Bacteria</option>
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48 <option value="Viruses">Viruses</option>
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49 </param>
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50 <param name="gcode" type="integer" value="0" min="0" max="23" label="Genetic code" help="Overrides the annotation mode option if set to > 0"/>
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51 <param name="gram" type="select" display="radio" label="Gram">
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52 <option selected="true" value="none">N/A</option>
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53 <option value="pos">positive</option>
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54 <option value="neg">negative</option>
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55 </param>
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56 <param name="usegenus" type="boolean" truevalue="--usegenus" falsevalue="" checked="false" label="Use genus-specific BLAST databases" />
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57 <param name="metagenome" type="boolean" truevalue="--metagenome" falsevalue="" checked="false" label="Improve gene predictions for highly fragmented genomes" />
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58 <param name="fast" type="boolean" truevalue="--fast" falsevalue="" checked="false" label="Fast mode - skip CDS /product searching" />
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59 <param name="cpus" type="integer" value="0" min="0" label="Number of CPUs to use [0=all] " />
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60 <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" />
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61 <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" />
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62 <param name="rfam" type="boolean" truevalue="--rfam" falsevalue="" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
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63 </inputs>
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64 <outputs>
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65 <data name="out_gff" format="gff" label="GFF" from_work_dir="outdir/prokka.gff"/>
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66 <data name="out_genbank" format="genbank" label="Genbank" from_work_dir="outdir/prokka.gbk"/>
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67 <data name="out_faa" format="fasta" label="Proteins (fasta)" from_work_dir="outdir/prokka.faa"/>
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68 <data name="out_ffn" format="fasta" label="Protein coding genes (fasta)" from_work_dir="outdir/prokka.ffn"/>
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69 <data name="out_fna" format="fasta" label="Genome (fasta)" from_work_dir="outdir/prokka.fna"/>
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70 <data name="out_fsa" format="fasta" label="Genbank submission (fasta)" from_work_dir="outdir/prokka.fsa"/>
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71 <data name="out_sqn" format="txt" label="Genbank submission (sqn)" from_work_dir="outdir/prokka.sqn"/>
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72 <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/>
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73 <data name="out_log" format="txt" label="Log" from_work_dir="outdir/prokka.log"/>
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74 <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
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75 </outputs>
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76 <stdio>
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77 <exit_code range="1:" level="fatal" description="Error" />
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78 </stdio>
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79 <help>
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80 **What it does**
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81
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82 This wrapper runs prokka, a tool to rapidly annotate prokaryotic genomes. For more information see the tool's homepage: http://www.vicbioinformatics.com/software.prokka.shtml
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83
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84 **License**
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85
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86 prokka is developed by Torsten Seemann at Victorian Bioinformatics Consortium http://www.bioinformatics.net.au/. prokka is released under GPLv3 or later.
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87
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88 This wrapper is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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89
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90 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
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91
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92 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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93 </help>
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94 </tool> |
