# HG changeset patch
# User sanbi-uwc
# Date 1537275342 14400
# Node ID 1f460ad509b68cbea049e5894fde72d8cf969ca7
# Parent  1a00583b6b2c28831d52ea0e3cb604cc60d5571a
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty

diff -r 1a00583b6b2c -r 1f460ad509b6 shapeit_phase.xml
--- a/shapeit_phase.xml	Tue Sep 18 08:48:52 2018 -0400
+++ b/shapeit_phase.xml	Tue Sep 18 08:55:42 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="shapeit_phase" name="shapeit_phase" version="0.15.0">
+<tool id="shapeit_phase" name="shapeit_phase" version="0.16.0">
     <description>genomic data with or without reference panel</description>
     <requirements>
         <requirement type="package" version="2.r837">shapeit</requirement>
@@ -7,7 +7,7 @@
         <exit_code range="1:" />
     </stdio>
 
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         #if str($input_files.input_type_select) == 'plink_bed_bim_fam_list':
           ln -s '${input_files.plink_bed_etc_list[0]}' input.plink_bed &&
           ln -s '${input_files.plink_bed_etc_list[1]}' input.plink_bim && 
@@ -182,12 +182,13 @@
           --output-log $out_log
         #else
           --output-log output
-          && mv output.mendel.log $out_log
+          | 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
         #end if
+        # NOTE that in check mode we are ignoring the error related to panel misalignment
     ]]></command>
-
     <inputs>
       <param name="check_mode" type="boolean" truevalue="-check" falsevalue="" label="Run in -check mode (check data)" />
       <conditional name="input_files">