--- a/prokka.xml	Tue Mar 21 10:13:06 2017 -0400
+++ b/prokka.xml	Wed Mar 28 12:38:42 2018 -0400
@@ -1,14 +1,11 @@
-<tool id="prokka" name="Prokka" version="1.12.0">
-    <description>prokaryotic genome annotation</description>
+<tool id="prokka" name="Prokka" version="1.13">
+    <description>Prokaryotic genome annotation</description>
     <requirements>
-        <requirement type="package" version="1.12">prokka</requirement>
+        <requirement type="package" version="1.13">prokka</requirement>
     </requirements>
-    <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+
     <version_command>prokka --version</version_command>
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
 prokka
 --cpus \${GALAXY_SLOTS:-8}
 --quiet ## to avoid non-error messages written to stderr
@@ -77,7 +74,7 @@
     ]]></command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
-        <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
+        <param name="locustag" type="text" value="" label="Locus tag prefix (--locustag)" />
         <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" />
         <param name="gffver" type="select" label="GFF version (--gffver)">
             <option value="3">3</option>
@@ -139,6 +136,7 @@
             <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc. (.sqn)</option>
             <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option>
             <option value="tbl" selected="True">Feature Table file (.tbl)</option>
+            <option value="tsv" selected="True">Annotations in tabular format including COGs etc.</option>
             <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option>
             <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option>
         </param>
@@ -169,6 +167,9 @@
         <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
              <filter>outputs and 'tbl' in outputs</filter>
         </data>
+        <data name="out_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv" from_work_dir="outdir/prokka.tsv">
+             <filter>outputs and 'tsv' in outputs</filter>
+        </data>
         <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
              <filter>outputs and 'err' in outputs</filter>
         </data>
@@ -180,7 +181,7 @@
     <tests>
         <test>
             <param name="input" ftype="fasta" value="phiX174.fasta" />
-            <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" />
+            <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" />
             <output name="out_gff" file="out.gff" />
             <output name="out_gbk" file="out.gbk" lines_diff="14" />
             <output name="out_fna" file="out.fna" />
@@ -189,6 +190,7 @@
             <output name="out_sqn" file="out.sqn" lines_diff="84" />
             <output name="out_fsa" file="out.fsa" />
             <output name="out_tbl" file="out.tbl" />
+            <output name="out_tsv" file="out.tsv" />
             <output name="out_err" file="out.err" />
             <output name="out_txt" file="out.txt" />
             <output name="out_log">
@@ -211,7 +213,7 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_, 2018 `Galaxy IUC` and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _Earlham Institute: http://earlham.ac.uk/