# HG changeset patch
# User devteam
# Date 1506793010 14400
# Node ID b59a6178a6e0bb5d120bf130ee98750638bad183
# Parent  774491f4a07422aa181b31e7457caa32c742707e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit dead2eaab58698fe02b8bb068f8d859eba551e8d

diff -r 774491f4a074 -r b59a6178a6e0 bwa-mem.xml
--- a/bwa-mem.xml	Thu Jun 01 11:38:11 2017 -0400
+++ b/bwa-mem.xml	Sat Sep 30 13:36:50 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2">
+<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.0">
   <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
   <macros>
     <import>read_group_macros.xml</import>
@@ -63,6 +63,7 @@
         ${analysis_type.io_options.V}
         ${analysis_type.io_options.Y}
         ${analysis_type.io_options.M}
+        ${analysis_type.io_options.five}
       #end if
 
     #end if
@@ -226,6 +227,7 @@
             <option value="do_not_set" selected="True">Do not set</option>
           </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 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 774491f4a074 -r b59a6178a6e0 bwa_macros.xml
--- a/bwa_macros.xml	Thu Jun 01 11:38:11 2017 -0400
+++ b/bwa_macros.xml	Sat Sep 30 13:36:50 2017 -0400
@@ -1,7 +1,7 @@
 <macros>
   <import>read_group_macros.xml</import>
 
-  <token name="@VERSION@">0.7.15</token>
+  <token name="@VERSION@">0.7.16</token>
 
   <token name="@set_rg_string@">
       #set $rg_string = "@RG\\tID:" + str($rg_id)
@@ -35,7 +35,7 @@
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@VERSION@">bwa</requirement>
-      <requirement type="package" version="1.3.1">samtools</requirement>
+      <requirement type="package" version="1.5">samtools</requirement>
     </requirements>
   </xml>
 
diff -r 774491f4a074 -r b59a6178a6e0 test-data/bwa-aln-test1-fasta.bam
Binary file test-data/bwa-aln-test1-fasta.bam has changed
diff -r 774491f4a074 -r b59a6178a6e0 test-data/bwa-aln-test1.bam
Binary file test-data/bwa-aln-test1.bam has changed
diff -r 774491f4a074 -r b59a6178a6e0 test-data/bwa-aln-test2.bam
Binary file test-data/bwa-aln-test2.bam has changed
diff -r 774491f4a074 -r b59a6178a6e0 test-data/bwa-aln-test3.bam
Binary file test-data/bwa-aln-test3.bam has changed
diff -r 774491f4a074 -r b59a6178a6e0 test-data/bwa-mem-test1-fasta.bam
Binary file test-data/bwa-mem-test1-fasta.bam has changed
diff -r 774491f4a074 -r b59a6178a6e0 test-data/bwa-mem-test1.bam
Binary file test-data/bwa-mem-test1.bam has changed
diff -r 774491f4a074 -r b59a6178a6e0 test-data/bwa-mem-test2.bam
Binary file test-data/bwa-mem-test2.bam has changed