# HG changeset patch
# User sanbi-uwc
# Date 1537278566 14400
# Node ID d3515c2a3f51b3f7b3814bd7e2ab1fd077b66d66
# Parent  1f460ad509b68cbea049e5894fde72d8cf969ca7
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty

diff -r 1f460ad509b6 -r d3515c2a3f51 shapeit_phase.xml
--- a/shapeit_phase.xml	Tue Sep 18 08:55:42 2018 -0400
+++ b/shapeit_phase.xml	Tue Sep 18 09:49:26 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="shapeit_phase" name="shapeit_phase" version="0.16.0">
+<tool id="shapeit_phase" name="shapeit_phase" version="0.17.0">
     <description>genomic data with or without reference panel</description>
     <requirements>
         <requirement type="package" version="2.r837">shapeit</requirement>
@@ -182,10 +182,10 @@
           --output-log $out_log
         #else
           --output-log output
-          | grep -v 'ERROR: Reference and Main panels are not well aligned:'
-          ; mv output.mendel.log $out_log
-          && mv output.mendel.snp.strand $out_strand
-          && mv output.mendel.snp.strand.exclude $out_exclude
+          | grep -v 'ERROR:.* Reference and Main panels are not well aligned:'
+          ; mv output.log $out_log
+          && mv output.snp.strand $out_strand
+          && mv output.snp.strand.exclude $out_exclude
         #end if
         # NOTE that in check mode we are ignoring the error related to panel misalignment
     ]]></command>