--- a/callaavar.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/callaavar.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,15 +1,27 @@
-<tool id="aavariants" name="Amino Acid Variants" version="0.4.2">
+<tool id="aavariants" name="Amino Acid Variants" version="0.5.1">
     <description>Identifies amino acid 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[
 
         ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
-        quasitools call aavar $input_bam $ref_file $var_file $input_genes
+		quasitools call aavar $input_bam $ref_file $input_genes 
+		
+		#if $var_file:
+			$var_file 
+		#end if
 
         #if $mutation_db:
-          $mutation_db
+        	$mutation_db
+        #end if
+
+		#if $min_freq:
+			-f $min_freq 
+		#end if
+
+		#if $error_rate:
+            -e $error_rate
         #end if
 
         -o output.vcf
@@ -18,10 +30,11 @@
     <inputs>
         <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
         <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
-        <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" />
         <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
+		<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." />
         <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." />
         <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." />
+        <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/>
     </inputs>
     <outputs>
         <data format="vcf" name="output" from_work_dir="output.vcf" />
@@ -51,9 +64,19 @@
 Amino Acid Variants
 ===================
 
-Identifies amino acid mutations.
+Identifies amino acid mutations for a BAM file.
+
+
 
     ]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolscallaavar,
+			title = {quasitools callaavar},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>