# HG changeset patch
# User iuc
# Date 1567726556 14400
# Node ID 086ba7b646e5486bf3325524491f83a8a861a31f
# Parent  6def3ba376a738becf79171e4262cc8e6574fe0c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"

diff -r 6def3ba376a7 -r 086ba7b646e5 bwa-mem.xml
--- a/bwa-mem.xml	Tue Apr 10 18:40:10 2018 -0400
+++ b/bwa-mem.xml	Thu Sep 05 19:35:56 2019 -0400
@@ -106,7 +106,7 @@
     '${fastq_input.fastq_input1}'
 #end if
 
-| samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output'
+| samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
     ]]></command>
 
     <inputs>
diff -r 6def3ba376a7 -r 086ba7b646e5 bwa.xml
--- a/bwa.xml	Tue Apr 10 18:40:10 2018 -0400
+++ b/bwa.xml	Thu Sep 05 19:35:56 2019 -0400
@@ -209,7 +209,7 @@
   '${reference_fasta_filename}' first.sai '${input_type.bam_input}'
 #end if
 
-| samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output'
+| samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
 ]]>
     </command>
 
diff -r 6def3ba376a7 -r 086ba7b646e5 read_group_macros.xml
--- a/read_group_macros.xml	Tue Apr 10 18:40:10 2018 -0400
+++ b/read_group_macros.xml	Thu Sep 05 19:35:56 2019 -0400
@@ -242,7 +242,7 @@
         <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
     </xml>
     <xml name="read_group_pu_required_param">
-        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
+        <param name="PU" type="text" value="run" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
     </xml>
     <!-- Only ID is required - all groups available -->
     <xml name="read_group_inputs_spec">