--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prokka.xml	Tue Sep 03 10:15:54 2013 -0400
@@ -0,0 +1,94 @@
+<tool id="prokka" name="prokka" version="0.1">
+  <description>prokaryotic genome annotation</description>
+  <requirements>
+    <requirement type="package" version="1.6">prokka</requirement>
+    <requirement type="package" version="1.2.36">aragorn</requirement>
+    <requirement type="package" version="1.2">rnammer</requirement>
+    <requirement type="package" version="2.60">prodigal</requirement>
+    <requirement type="package" version="4.1">signalp</requirement>
+    <requirement type="package" version="3.0">infernal</requirement>
+    <requirement type="package" version="3.1">hmmer</requirement>
+    <requirement type="package">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
+  --increment $increment
+  --centre $centre
+  --genus $genus --species $species --strain $strain
+  --kingdom $kingdom
+  --gcode $gcode
+  #if $gram != "none"
+  --gram $gram
+  #end if
+  $usegenus
+  $metagenome
+  $fast
+  --cpus $cpus
+  --mincontig $mincontig
+  --evalue $evalue
+  $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="centre" type="text" value="molevoUU" 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="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="0" min="0" label="Number of CPUs to use [0=all] " />
+    <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!)" />
+  </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" />
+  </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>
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