--- a/snippy.xml	Mon Mar 18 10:59:29 2019 -0400
+++ b/snippy.xml	Tue Apr 02 17:21:50 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
+<tool id="snippy" name="snippy" version="@VERSION@+galaxy2">
   <description>
       Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
   </description>
@@ -40,16 +40,13 @@
             #if str( $fastq_input.fastq_input_selector ) == "paired"
                 --R1 '$fastq_input.fastq_input1'
                 --R2 '$fastq_input.fastq_input2'
-            #end if
-            #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
+            #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
                 --R1 '$fastq_input.fastq_input.forward'
                 --R2 '$fastq_input.fastq_input.reverse'
-            #end if
-            #if str( $fastq_input.fastq_input_selector ) == "single"
-                --se '$fastq_input.fastq_input'
-            #end if
-            #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
-                --peil '$fastq_input.fastq_input'
+            #elif str( $fastq_input.fastq_input_selector ) == "single"
+                --se '$fastq_input.fastq_input_single'
+            #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
+                --peil '$fastq_input.fastq_input_interleaved'
             #end if
 
         &&
@@ -59,8 +56,10 @@
             #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
         #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
             #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
-        #else
-            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
+        #elif str( $fastq_input.fastq_input_selector ) == "single"
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
+        #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
         #end if
 
         mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
@@ -88,13 +87,13 @@
                 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
             </when>
             <when value="single">
-                <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
+                <param name="fastq_input_single" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
             </when>
             <when value="paired_collection">
                 <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
             </when>
             <when value="paired_iv">
-                <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
+                <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
             </when>
         </conditional>
 
@@ -200,6 +199,16 @@
             <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
         </test>
 
+        <test> <!-- test 3 - fasta ref one snp single -->
+            <param name="ref" value="reference.fasta" ftype="fasta" />
+            <param name="fastq_input_selector" value="single" />
+            <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
+            <param name="mincov" value="2" />
+            <param name="minqual" value="60" />
+            <param name="outputs" value="outgff,outsum" />
+            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
+            <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
+        </test>
     </tests>
 
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_2_fna_ref_mincov_2_minqual_60.snps.gff	Tue Apr 02 17:21:50 2019 -0400
@@ -0,0 +1,2 @@
+##gff-version 3
+reference	snippy:4.3.6	variation	4	4	.	.	0	note=snp A=>T T:5 A:0