# HG changeset patch
# User devteam
# Date 1511273466 18000
# Node ID a4d167793afa75504f1d097f3f76e5e5d05e92eb
# Parent  b59a6178a6e0bb5d120bf130ee98750638bad183
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit e1191c87a0fccfafa0f23c3bd09f416a6700b387

diff -r b59a6178a6e0 -r a4d167793afa bwa-mem.xml
--- a/bwa-mem.xml	Sat Sep 30 13:36:50 2017 -0400
+++ b/bwa-mem.xml	Tue Nov 21 09:11:06 2017 -0500
@@ -64,6 +64,7 @@
         ${analysis_type.io_options.Y}
         ${analysis_type.io_options.M}
         ${analysis_type.io_options.five}
+        ${analysis_type.io_options.q}
       #end if
 
     #end if
@@ -228,6 +229,7 @@
           </param>
           <when value="set">
             <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/>
+            <param argument="-q" type="boolean" truevalue="-q" falsevalue="" label="Don't lower MAPQ for split alignment" help="By default the MAPQ score of a supplementary alignment will be lowered to the primary alignment score."/>
             <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
             <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" />
             <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>
diff -r b59a6178a6e0 -r a4d167793afa bwa_macros.xml
--- a/bwa_macros.xml	Sat Sep 30 13:36:50 2017 -0400
+++ b/bwa_macros.xml	Tue Nov 21 09:11:06 2017 -0500
@@ -1,7 +1,7 @@
 <macros>
   <import>read_group_macros.xml</import>
 
-  <token name="@VERSION@">0.7.16</token>
+  <token name="@VERSION@">0.7.17</token>
 
   <token name="@set_rg_string@">
       #set $rg_string = "@RG\\tID:" + str($rg_id)