--- a/snippy.xml	Tue Mar 12 17:37:29 2019 -0400
+++ b/snippy.xml	Mon Jun 17 16:42:39 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>
@@ -18,7 +18,8 @@
         #end if
         snippy
             --outdir 'out'
-            --cpus "\${GALAXY_SLOTS:-1}"
+            --cpus \${GALAXY_SLOTS:-1}
+            --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
             #if $ref.is_of_type("fasta")
                 --ref 'ref.fna'
             #end if
@@ -33,22 +34,19 @@
                 --rgid '$adv.rgid'
             #end if
             #if $adv.bwaopt
-                --bwaopt '$advanced.bwaopt'
+                --bwaopt '$adv.bwaopt'
             #end if
 
             #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
 
         &&
@@ -58,8 +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}/ &&
@@ -87,13 +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>
 
@@ -101,10 +101,10 @@
             <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
             <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
             <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
-	    <param name="minqual" type="float" value="100.0" label="Minumum QUALITY in VCF column 6" help="Minumum QUALITY in VCF column 6" />
+            <param name="minqual" type="float" value="100.0" label="Minumum QUALITY in VCF column 6" help="Minumum QUALITY in VCF column 6" />
             <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
             <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
-	    <param name="rename_cons" type="boolean" truevalue="rename_cons" falsevalue="" help="When producing an output of the reference genome with variants instantiated, edit the header so that it is named after the input VCF" />
+            <param name="rename_cons" type="boolean" truevalue="rename_cons" falsevalue="" help="When producing an output of the reference genome with variants instantiated, edit the header so that it is named after the input VCF" />
         </section>
 
         <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
@@ -167,8 +167,8 @@
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />
-            <output name="snpsum" ftype="tabular" file="fna_ref_a/snps.txt" lines_diff="6" />
-            <output name="snpgff" ftype="gff3" file="fna_ref_a/snps.gff" />
+            <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
+            <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" />
         </test>
 
         <test> <!-- test 1 - fasta ref one snp -->
@@ -179,8 +179,8 @@
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />
-            <output name="snpsum" ftype="tabular" file="fna_ref_b/snps.txt" lines_diff="6" />
-            <output name="snpgff" ftype="gff3" file="fna_ref_b/snps.gff" />
+            <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_fna_ref_mincov_2_minqual_60.snps.gff" />
         </test>
 
         <test> <!-- test 2 - fasta ref one snp paired_collection -->
@@ -195,10 +195,20 @@
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />
-            <output name="snpsum" ftype="tabular" file="fna_ref_b/snps.txt" lines_diff="6" />
-            <output name="snpgff" ftype="gff3" file="fna_ref_b/snps.gff" />
+            <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_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>