--- a/prokka.xml	Thu Jan 09 16:49:50 2014 -0500
+++ b/prokka.xml	Mon Oct 27 06:45:52 2014 -0400
@@ -1,16 +1,16 @@
-<tool id="prokka" name="Prokka" version="1.3.0">
+<tool id="prokka" name="Prokka" version="1.4.0">
   <description>prokaryotic genome annotation</description>
   <requirements>
     <requirement type="package" version="2.2.28">blast+</requirement>
     <requirement type="package" version="3.1b1">hmmer</requirement>
     <requirement type="package" version="1.2.36">aragorn</requirement>
     <requirement type="package" version="2.60">prodigal</requirement>
-    <requirement type="package" version="22.4">tbl2asn</requirement>
+    <requirement type="package" version="23.7">tbl2asn</requirement>
     <requirement type="package" version="20131122">gnu_parallel</requirement>
-    <requirement type="package" version="0.3">barrnap</requirement>
+    <requirement type="package" version="0.5">barrnap</requirement>
     <requirement type="package" version="1.1">infernal</requirement>
-    <requirement type="package" version="0.1.4">minced</requirement>
-    <requirement type="package" version="1.8">prokka</requirement>
+    <requirement type="package" version="0.1.6">minced</requirement>
+    <requirement type="package" version="1.10">prokka</requirement>
   </requirements>
   <version_command>prokka --version</version_command>
   <command>
@@ -57,6 +57,9 @@
     #if $usegenus
       --usegenus
     #end if
+    #if $proteins
+      --proteins $proteins
+    #end if
     #if $metagenome
       --metagenome
     #end if
@@ -77,9 +80,13 @@
     #end if
     $input
   </command>
+  <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
   <inputs>
     <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
-    <param name="locustag" type="text" value="PROKKA" optional="true" label="Locus tag prefix (--locustag)" />
+    <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
     <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)">
       <validator type="in_range" min="1" />
     </param>
@@ -99,11 +106,11 @@
       </when>
       <when value="yes" />
     </conditional>
-    <param name="centre" type="text" value="" optional="true" label="Sequencing centre ID (--centre)" />
-    <param name="genus" type="text" value="" optional="true" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
-    <param name="species" type="text" value="" optional="true" label="Species name (--species)" />
-    <param name="strain" type="text" value="" optional="true" label="Strain name (--strain)" />
-    <param name="plasmid" type="text" value="" optional="true" label="Plasmid name or identifier (--plasmid)" />
+    <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
+    <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
+    <param name="species" type="text" value="" label="Species name (--species)" />
+    <param name="strain" type="text" value="" label="Strain name (--strain)" />
+    <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
     <conditional name="kingdom">
       <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
         <option value="Archaea">Archaea</option>
@@ -126,6 +133,7 @@
       </when>
     </conditional>
     <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" />
+    <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
     <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
     <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
     <param name="evalue" type="float" value="1e-06" optional="true" label="Similarity e-value cut-off">
@@ -184,18 +192,27 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_, Lionel Guy and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_, © 2013 Lionel Guy and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _MIT license: http://opensource.org/licenses/MIT
 
-If you use this tool in Galaxy, please cite |Cuccuru2013|_.
-
-.. |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*
-.. _Cuccuru2013: http://orione.crs4.it/
-
-This tool uses `Prokka`_, which is licensed separately. Please cite Seemann, T. (2013) Prokka: Rapid Prokaryotic Genome Annotation. *Submitted*
+You can use this tool only if you agree to the license terms of: `Prokka`_.
 
 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
+
+If you use this tool, please cite:
+
+- |Cuccuru2014|_
+- |Seemann2014|_.
+
+.. |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
+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
+.. |Seemann2014| replace:: Seemann, T. (2014) Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 30(14), 2068-2069
+.. _Seemann2014: http://bioinformatics.oxfordjournals.org/content/30/14/2068
   </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu135</citation>
+    <citation type="doi">10.1093/bioinformatics/btu153</citation>
+  </citations>
 </tool>