# HG changeset patch
# User iuc
# Date 1591344772 14400
# Node ID 5d6ed46cc101f2f3d200eb146133f91161094f01
# Parent  cb903c9dc33d2d299b1ff3617989746f5a0bc8de
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 47276c84cd0cd40084b7ccdf2e22c620ee1c10f6"

diff -r cb903c9dc33d -r 5d6ed46cc101 ivar_trim.xml
--- a/ivar_trim.xml	Wed Apr 22 06:05:42 2020 -0400
+++ b/ivar_trim.xml	Fri Jun 05 04:12:52 2020 -0400
@@ -20,8 +20,7 @@
         -s $window_width
         $inc_primers
         -p trimmed &&
-        samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam &&
-        samtools index -@ \${GALAXY_SLOTS:-1} trimmed.sorted.bam
+        samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam
     ]]>    </command>
     <inputs>
         <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
diff -r cb903c9dc33d -r 5d6ed46cc101 macros.xml
--- a/macros.xml	Wed Apr 22 06:05:42 2020 -0400
+++ b/macros.xml	Fri Jun 05 04:12:52 2020 -0400
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@VERSION@">1.2.1</token>
+  <token name="@VERSION@">1.2.2</token>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@VERSION@">ivar</requirement>
diff -r cb903c9dc33d -r 5d6ed46cc101 test-data/sars-cov-2/sars_cov2_trimmed.bam
Binary file test-data/sars-cov-2/sars_cov2_trimmed.bam has changed