--- a/snippy.xml	Tue Jan 22 14:48:36 2019 -0500
+++ b/snippy.xml	Thu Jan 24 14:19:32 2019 -0500
@@ -11,19 +11,19 @@
     <command detect_errors="exit_code"><![CDATA[
 
         #if $ref.is_of_type("fasta")
-            cp '$ref' 'ref.fna' &&
+            cp '$ref' 'foo.fna' &&
         #end if
         #if $ref.is_of_type("genbank")
-            cp '$ref' 'ref.gbk' &&
+            cp '$ref' 'foo.gbk' &&
         #end if
         snippy
             --outdir 'out'
             --cpus "\${GALAXY_SLOTS:-1}"
             #if $ref.is_of_type("fasta")
-                --ref 'ref.fna'
+                --ref 'foo.fna'
             #end if
             #if $ref.is_of_type("genbank")
-                --ref 'ref.gbk'
+                --ref 'foo.gbk'
             #end if
             --mapqual $adv.mapqual
             --mincov $adv.mincov
@@ -36,12 +36,12 @@
             #end if
 
             #if str( $fastq_input.fastq_input_selector ) == "paired"
-                --R1 '$fastq_input.fastq_input1'
-                --R2 '$fastq_input.fastq_input2'
+                --pe1 '$fastq_input.fastq_input1'
+                --pe2 '$fastq_input.fastq_input2'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
-                --R1 '$fastq_input.fastq_input.forward'
-                --R2 '$fastq_input.fastq_input.reverse'
+                --pe1 '$fastq_input.fastq_input.forward'
+                --pe2 '$fastq_input.fastq_input.reverse'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "single"
                 --se '$fastq_input.fastq_input'
@@ -52,14 +52,18 @@
 
         &&
 
+        gunzip out/snps.depth.gz
+
+        &&
+
         #import re
-	#if str( $fastq_input.fastq_input_selector ) == "paired"
-	    #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
-	#else
+        #if str( $fastq_input.fastq_input_selector ) == "paired"
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
+        #else
             #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
-	#end if
-        mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
+        #end if
 
+        mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa ${dir_name}/ &&
         tar -czf out.tgz ${dir_name}
 
 
@@ -204,6 +208,20 @@
             <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" />
         </test>
 
+        <test> <!-- test 6 - fasta ref default paired_collection -->
+	    <param name="ref" value="wildtype.fna" ftype="fasta" />
+            <param name="fastq_input_selector" value="paired_collection" />
+            <param name="fastq_input">
+                <collection type="paired">
+                    <element name="forward" ftype="fastqsanger" value="mutant_R1.fastq" />
+                    <element name="reverse" ftype="fastqsanger" value="mutant_R2.fastq" />
+                </collection>
+            </param>
+            <param name="outputs" value="outgff,outsum" />
+            <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
+            <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
+        </test>
+
     </tests>