--- a/snippy-core.xml	Sun Dec 01 13:06:05 2019 -0500
+++ b/snippy-core.xml	Mon Jan 27 21:50:49 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy1">
+<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy2">
     <description>
         Combine multiple Snippy outputs into a core SNP alignment
     </description>
@@ -9,14 +9,14 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @REFERENCE_SOURCE_FILE@
+        mkdir 'snippy_dirs' && cd 'snippy_dirs' &&
         #for $indir in $indirs
-            #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0]
-            mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 &&
+            tar -xf '$indir' -C . &&
         #end for
-        #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs])
+        cd - &&
         snippy-core
             @REFERENCE_COMMAND@
-            ${snippy_dirs}
+            snippy_dirs/*
     ]]></command>
 
     <inputs>

--- a/snippy.xml	Sun Dec 01 13:06:05 2019 -0500
+++ b/snippy.xml	Mon Jan 27 21:50:49 2020 -0500
@@ -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>
@@ -12,8 +12,19 @@
 
         @REFERENCE_SOURCE_FILE@
 
+        #import re
+        #if str( $fastq_input.fastq_input_selector ) == "paired"
+            #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)
+        #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_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
+        #end if
+
         snippy
-            --outdir 'out'
+            --outdir '${dir_name}'
             --cpus \${GALAXY_SLOTS:-1}
             --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
             @REFERENCE_COMMAND@
@@ -40,26 +51,12 @@
                 --peil '$fastq_input.fastq_input_interleaved'
             #end if
 
-        &&
-
-        #import re
-        #if str( $fastq_input.fastq_input_selector ) == "paired"
-            #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)
-        #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_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
+        #if "outcon" in str($outputs) and $adv.rename_cons
+          && sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa'
         #end if
 
-        mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
-		tar -czf out.tgz ${dir_name}
-        #if "outcon" in str($outputs) and $adv.rename_cons
-          && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
-        #end if
-
-
+        && cp -r '${dir_name}' out
+        && tar -czf out.tgz '${dir_name}'
     ]]>    </command>
 
     <inputs>