# HG changeset patch
# User dfornika
# Date 1560895368 14400
# Node ID 15d5dd95daf228385e521fdbec4069dc76216589
# Parent  ae9dffe91f2094ade5e3c90613ec285b24c21859
planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty

diff -r ae9dffe91f20 -r 15d5dd95daf2 snippy.xml
--- a/snippy.xml	Tue Jun 18 16:08:43 2019 -0400
+++ b/snippy.xml	Tue Jun 18 18:02:48 2019 -0400
@@ -62,7 +62,9 @@
 
         &&
 
-        tar -czf out.tgz ${dir_name}
+	cp -r '$dir_name' 'out' &&
+
+        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
@@ -123,31 +125,31 @@
 
     <outputs>
 
-        <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="${dir_name}/snps.vcf">
+        <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
             <filter>outputs and 'outvcf' in outputs</filter>
         </data>
-        <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="${dir_name}/snps.gff">
+        <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
             <filter>outputs and 'outgff' in outputs</filter>
         </data>
-        <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="${dir_name}/snps.tab">
+        <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
             <filter>outputs and 'outtab' in outputs</filter>
         </data>
-        <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="${dir_name}/snps.txt">
+        <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
             <filter>outputs and 'outsum' in outputs</filter>
         </data>
-        <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="${dir_name}/snps.log">
+        <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
             <filter>outputs and 'outlog' in outputs</filter>
         </data>
-        <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="${dir_name}/snps.aligned.fa">
+        <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
             <filter>outputs and 'outaln' in outputs</filter>
         </data>
-        <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="${dir_name}/snps.consensus.fa">
+        <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
             <filter>outputs and 'outcon' in outputs</filter>
         </data>
-        <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="${dir_name}/snps.depth">
+        <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth">
             <filter>outputs and 'outdep' in outputs</filter>
         </data>
-        <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="${dir_name}/snps.bam">
+        <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
             <filter>outputs and 'outbam' in outputs</filter>
         </data>
         <data format="tar" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">