--- a/prokka.xml	Tue Sep 03 10:15:54 2013 -0400
+++ b/prokka.xml	Wed Sep 04 11:33:13 2013 -0400
@@ -1,14 +1,14 @@
-<tool id="prokka" name="prokka" version="0.1">
+<tool id="prokka" name="prokka" version="0.2">
   <description>prokaryotic genome annotation</description>
   <requirements>
-    <requirement type="package" version="1.6">prokka</requirement>
+    <requirement type="package" version="1.7">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" 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>
@@ -17,12 +17,26 @@
   --prefix prokka
   $addgenes
   --locustag $locustag
+  $compliant
   --increment $increment
+  #if str($centre) != ""
   --centre $centre
-  --genus $genus --species $species --strain $strain
+  #end if
+  #if str($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"
+  #if $gram != "None"
   --gram $gram
   #end if
   $usegenus
@@ -31,6 +45,9 @@
   --cpus $cpus
   --mincontig $mincontig
   --evalue $evalue
+  $rfam
+  $norrna
+  $notrna
   $input
   </command>
   <inputs>
@@ -38,10 +55,12 @@
     <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="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>
@@ -60,6 +79,8 @@
     <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"/>
@@ -74,8 +95,13 @@
     <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>  
+    <!--<exit_code range="1:" level="fatal" description="Error" />-->
+    <regex match="not a readable non-empty FASTA file"
+	   source="stdout"
+	   level="fatal"
+	   description="Input file not a readable non-empty FASTA file" />
+  </stdio> 
+  
   <help>
 **What it does**