--- a/prokka.xml	Sat Oct 29 09:15:32 2016 -0400
+++ b/prokka.xml	Sat Oct 29 09:29:09 2016 -0400
@@ -130,17 +130,17 @@
         <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
         <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
 
-        <param name="outputs" type="select" multiple="true" label="Additional outputs">
-            <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations</option>
-            <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence</option>
-            <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences</option>
-            <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences</option>
-            <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS</option>
-            <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.</option>
-            <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines</option>
-            <option value="tbl" selected="True">Feature Table file</option>
-            <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report</option>
-            <option value="txt" selected="True">Statistics relating to the annotated features found</option>
+        <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
+            <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option>
+            <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence (.gbk)</option>
+            <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>
+            <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option>
+            <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option>
+            <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="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>
 
     </inputs>
@@ -207,30 +207,7 @@
 
 **Output files**
 
-Prokka creates several output files:
-
-gff
-    This is the master annotation in GFF format, containing both sequences and annotations
-gbk
-    This is a standard GenBank file derived from the master .gff . If the input to prokka was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence
-fna
-    Nucleotide FASTA file of the input contig sequences
-faa
-    Protein FASTA file of the translated CDS sequences
-ffn
-    Nucleotide FASTA file of all the annotated sequences, not just CDS
-sqn
-    An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.
-fsa
-    Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines
-tbl
-    Feature Table file, used by "tbl2asn" to create the .sqn file
-err
-    Unacceptable annotations - the NCBI discrepancy report
-log
-    Contains all the output that Prokka produced during its run
-txt
-    Statistics relating to the annotated features found
+Prokka creates several output files, which are described in the **Additional outputs** section above.
 
 **License and citation**