# HG changeset patch
# User lionelguy
# Date 1378367963 14400
# Node ID 5c289bf13a083d6099ec068b26135cc285b1a287
# Parent  bb07951d72dbdd6e31ade6144bac34a66967ce06
Uploaded

diff -r bb07951d72db -r 5c289bf13a08 prokka.xml
--- a/prokka.xml	Wed Sep 04 11:35:45 2013 -0400
+++ b/prokka.xml	Thu Sep 05 03:59:23 2013 -0400
@@ -75,7 +75,7 @@
     <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="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!)" />
@@ -95,11 +95,15 @@
     <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
   </outputs>
   <stdio>
-    <!--<exit_code range="1:" level="fatal" description="Error" />-->
+    <exit_code range="1:" level="fatal" description="Error" />
     <regex match="not a readable non-empty FASTA file"
-	   source="stdout"
+	   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" />
   </stdio> 
   
   <help>