# HG changeset patch
# User veg
# Date 1520532362 18000
# Node ID 787baac95405af08631817ddc8135c3aa145e1ad
# Parent  c6f0b318bc035f052cab83b5feb17acb61e9f39e
planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'1e1a1e37fa621df190621f5c95c00fb9d31d9a60\n'-dirty

diff -r c6f0b318bc03 -r 787baac95405 bealign.xml
--- a/bealign.xml	Thu Feb 22 15:48:40 2018 -0500
+++ b/bealign.xml	Thu Mar 08 13:06:02 2018 -0500
@@ -8,7 +8,7 @@
     <version_command>bealign --version</version_command>
     <command detect_errors="exit_code">
     <![CDATA[
-    bealign --reference $reference $advanced.expected_identity --alphabet $advanced.alphabet
+    bealign --reference '$select_reference.reference' $advanced.expected_identity --alphabet $advanced.alphabet
         --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
         #if $advanced.discard:
             $advanced.discard $advanced.discarded_reads