# HG changeset patch
# User jbarberoaparicio
# Date 1555578324 14400
# Node ID db0dad5b47d4fc3b10a63395a8bd52612c84f99c
# Parent  88bea560431e59e3d2cea383367c78f6261c6142
Uploaded

diff -r 88bea560431e -r db0dad5b47d4 roary/myTools/roary_tool.xml
--- 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