--- a/callcodonvar.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/callcodonvar.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="callcodonvar" name="Codon Variants" version="0.4.2">
+<tool id="callcodonvar" name="Codon Variants" version="0.5.1">
     <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
     <requirements>
-          <requirement type="package" version="0.4.2">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -10,6 +10,10 @@
         ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
         quasitools call codonvar $input_bam $ref_file $offset $input_genes
 
+		#if $var_file:
+			$var_file 
+		#end if
+
         #if $error_rate:
             -e $error_rate
         #end if
@@ -22,7 +26,8 @@
         <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
         <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/>
         <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
-        <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.01" help="Estimated sequencing error rate. Defaults to 0.01." />
+		<param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021." />
+		<param name="var_file" type="data" format="vcf" optional="true" label="Variants file" help="Not required. If not supplied, a variants file will be generated using the input bam file." />
     </inputs>
     <outputs>
         <data format="csv" name="output" from_work_dir="output.csv" />
@@ -52,5 +57,13 @@
 
     ]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolscallcodonvar,
+			title = {quasitools callcodonvar},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>