Mercurial > repos > iuc > snippy

changeset 8:32f2211eeec3 draft

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"planemo upload commit 5b41fad964a75dcdc794e90342144c3eccea16d7"
author iuc
date Sun, 01 Dec 2019 13:06:05 -0500
parents e32aac2299fb
children e4d0231d8595
files macros.xml snippy-core.xml snippy.xml
diffstat 3 files changed, 4 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri Nov 15 08:19:05 2019 -0500
+++ b/macros.xml	Sun Dec 01 13:06:05 2019 -0500
@@ -2,6 +2,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">snippy</requirement>
+            <requirement type="package" version="1.32">tar</requirement>
             <yield />
         </requirements>
     </xml>
--- a/snippy-core.xml	Fri Nov 15 08:19:05 2019 -0500
+++ b/snippy-core.xml	Sun Dec 01 13:06:05 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy0">
+<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy1">
     <description>
         Combine multiple Snippy outputs into a core SNP alignment
     </description>
--- a/snippy.xml	Fri Nov 15 08:19:05 2019 -0500
+++ b/snippy.xml	Sun Dec 01 13:06:05 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="snippy" name="snippy" version="@VERSION@+galaxy0">
+<tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
   <description>
       Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
     </description>
@@ -54,7 +54,7 @@
         #end if
 
         mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
-        tar -cf - ${dir_name} | gzip > out.tgz
+		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