# HG changeset patch
# User iuc
# Date 1610470706 0
# Node ID 09b2cdb7ace5083f78e1ee3c26b867297b976f4e
# Parent  749c918495f7986113fadb5126ec083fd78d3c3e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"

diff -r 749c918495f7 -r 09b2cdb7ace5 bowtie2_macros.xml
--- a/bowtie2_macros.xml	Fri Aug 23 13:24:25 2019 -0400
+++ b/bowtie2_macros.xml	Tue Jan 12 16:58:26 2021 +0000
@@ -1,4 +1,5 @@
 <macros>
+    <token name="@TOOL_VERSION@">2.4.2</token>
     <!-- Import this at the top of your command block and then
          define rg_auto_name. -->
     <token name="@define_read_group_helpers@">
diff -r 749c918495f7 -r 09b2cdb7ace5 bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Fri Aug 23 13:24:25 2019 -0400
+++ b/bowtie2_wrapper.xml	Tue Jan 12 16:58:26 2021 +0000
@@ -1,11 +1,11 @@
-<tool id="bowtie2" name="Bowtie2" version="2.3.4.3+galaxy0" profile="18.01">
+<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="18.01">
     <description>- map reads against reference genome</description>
     <macros>
         <import>bowtie2_macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="2.3.4.1">bowtie2</requirement>
-        <requirement type="package" version="1.9">samtools</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
+        <requirement type="package" version="1.11">samtools</requirement>
     </requirements>
     <version_command>bowtie2 --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -305,7 +305,7 @@
 
 ## output file
 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
-    | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
+    | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
 #else if $sam_options.reorder:
     | samtools view -bS - -o '$output'
 #else: