diff cpo_snippy.xml @ 5:698579246d0d draft

planemo upload

--- a/cpo_snippy.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_snippy.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,4 +1,5 @@
-<tool id="snippy" name="snippy" version="3.2">
+<tool id="cpo_snippy" name="CPO_Snippy" version="3.2">
+  <description>Modified Snippy v3.2 to support contig inputs for the cpo_prediction workflow</description>
   <requirements>
     <requirement type="package" version="3.2">snippy</requirement>
   </requirements>
@@ -32,7 +33,11 @@
 
       &&
 
-      tar -czf out.tgz out
+      #import re
+      #set $dir_name = re.sub('[^\w_]', '_', $input.element_identifier)
+      mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
+
+      tar -czf out.tgz ${dir_name}
 
 
     ]]>