Mercurial > repos > jbarberoaparicio > roary

changeset 21:db0dad5b47d4 draft

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Uploaded
author jbarberoaparicio
date Thu, 18 Apr 2019 05:05:24 -0400
parents 88bea560431e
children fa5639bff74f
files roary/myTools/roary_tool.xml
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/roary/myTools/roary_tool.xml	Thu Apr 18 04:36:46 2019 -0400
+++ b/roary/myTools/roary_tool.xml	Thu Apr 18 05:05:24 2019 -0400
@@ -8,7 +8,8 @@
     <command detect_errors="exit_code"><![CDATA[
         
         #for $counter, $gff in enumerate($gff_input.gffs)
-          cp $gff ${gff}.gff &&   
+          sample="$(cut -d'/' -f6 <<<'$gff')"
+          cp $gff ${sample}.gff &&   
         #end for
                 
         roary