<tool id="prokka" name="prokka" version="0.2">
  <description>prokaryotic genome annotation</description>
  <requirements>
    <requirement type="package" version="1.7">prokka</requirement>
    <requirement type="package" version="1.2.36">aragorn</requirement>
    <requirement type="package" version="2.60">prodigal</requirement>
    <!--<requirement type="package" version="0.1">package_barrnap_0_1</requirement>-->
    <requirement type="package" version="0.1">barrnap</requirement>
    <!-- <requirement type="package" version="4.1">signalp</requirement> -->
    <!-- <requirement type="package" version="3.0">infernal</requirement> -->
    <requirement type="package" version="3.1b1">hmmer</requirement>
    <requirement type="package" version="2.2.26+">blast+</requirement>
    <requirement type="package">tbl2asn</requirement>
  </requirements>
  <version_command>prokka --version</version_command>
  <command>prokka --outdir outdir --force 
  --quiet ## To avoid messages written to stderr and causing galaxy errors
  --prefix prokka
  $addgenes
  --locustag $locustag
  $compliant
  --increment $increment
  #if str($centre) != ""
  --centre $centre
  #end if
  #if str($genus) != ""
  --genus $genus 
  #end if 
  #if str($species) != ""
  --species $species 
  #end if 
  #if str($strain) != ""
  --strain $strain 
  #end if 
  #if str($plasmid) != ""
  --plasmid $plasmid
  #end if 
  --kingdom $kingdom
  --gcode $gcode
  #if $gram != "None"
  --gram $gram
  #end if
  $usegenus
  $metagenome
  $fast
  --cpus $cpus
  --mincontig $mincontig
  --evalue $evalue
  $rfam
  $norrna
  $notrna
  $input
  </command>
  <inputs>
    <param name="input" type="data" format="fasta" label="Contigs to annotate" />
    <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix"/>
    <param name="addgenes" type="boolean" truevalue="--addgenes" falsevalue="" checked="false" label="Add 'gene' features for each 'CDS' feature" />
    <param name="increment" type="integer" value="10" label="Locus tag counter increment" />
    <param name="compliant" type="boolean" truevalue="--compliant" falsevalue="" checked="false" label="Force Genbank/ENA/DDJB compliance: --genes --mincontiglen 200 --centre XXX" />
    <param name="centre" type="text" value="XXX" label="Locus tag prefix"/>
    <param name="genus" type="text" value="Genus" label="Genus name (will be used to aid annotation)"/>
    <param name="species" type="text" value="species" label="Species name"/>
    <param name="strain" type="text" value="strain" label="Strain name"/>
    <param name="plasmid" type="text" value="" label="Plasmid name or identifier"/>
    <param name="kingdom" type="select" display="radio" label="Annotation mode">
      <option value="Archaea">Archaea</option>
      <option value="Bacteria" selected="True">Bacteria</option>
      <option value="Viruses">Viruses</option>
    </param>
    <param name="gcode" type="integer" value="0" min="0" max="23" label="Genetic code" help="Overrides the annotation mode option if set to > 0"/>
    <param name="gram" type="select" display="radio" label="Gram">
      <option selected="true" value="none">N/A</option>
      <option value="pos">positive</option>
      <option value="neg">negative</option>
    </param>
    <param name="usegenus" type="boolean" truevalue="--usegenus" falsevalue="" checked="false" label="Use genus-specific BLAST databases" />
    <param name="metagenome" type="boolean" truevalue="--metagenome" falsevalue="" checked="false" label="Improve gene predictions for highly fragmented genomes" />
    <param name="fast" type="boolean" truevalue="--fast" falsevalue="" checked="false" label="Fast mode - skip CDS /product searching" />
    <param name="cpus" type="integer" value="4" min="1" label="Number of CPUs to use " />
    <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" />
    <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" />
    <param name="rfam" type="boolean" truevalue="--rfam" falsevalue="" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
    <param name="norrna" type="boolean" truevalue="--norrna" falsevalue="" checked="false" label="Don't run rRNA search" />
    <param name="notrna" type="boolean" truevalue="--notrna" falsevalue="" checked="false" label="Don't run tRNA search" />
  </inputs>
  <outputs>
    <data name="out_gff" format="gff" label="GFF" from_work_dir="outdir/prokka.gff"/>
    <data name="out_genbank" format="genbank" label="Genbank" from_work_dir="outdir/prokka.gbk"/>
    <data name="out_faa" format="fasta" label="Proteins (fasta)" from_work_dir="outdir/prokka.faa"/>
    <data name="out_ffn" format="fasta" label="Protein coding genes (fasta)" from_work_dir="outdir/prokka.ffn"/>
    <data name="out_fna" format="fasta" label="Genome (fasta)" from_work_dir="outdir/prokka.fna"/>
    <data name="out_fsa" format="fasta" label="Genbank submission (fasta)" from_work_dir="outdir/prokka.fsa"/>
    <data name="out_sqn" format="txt" label="Genbank submission (sqn)" from_work_dir="outdir/prokka.sqn"/>
    <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/>
    <data name="out_log" format="txt" label="Log" from_work_dir="outdir/prokka.log"/>
    <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
  </outputs>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
    <regex match="not a readable non-empty FASTA file"
	   source="both"
	   level="fatal"
	   description="Input file not a readable non-empty FASTA file" />
    <regex match="Illegal division by zero"
	   source="both"
	   level="fatal"
	   description="Illegal division by zero" />
    <regex match="no suitable sequence entries"
	   source="both"
	   level="fatal"
	   description="Input contains no suitable sequences" />
    <regex match="Can't find required"
	   source="both"
	   level="fatal"
	   description="Dependencies not available" />
   
  </stdio> 
  
  <help>
**What it does**

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

**License**

prokka is developed by  Torsten Seemann at Victorian Bioinformatics Consortium http://www.bioinformatics.net.au/. prokka is released under GPLv3 or later.

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.

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.

You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
  </help>
</tool>