Mercurial > repos > iuc > ivar_trim

diff ivar_trim.xml @ 3:5d6ed46cc101 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 47276c84cd0cd40084b7ccdf2e22c620ee1c10f6"
author iuc
date Fri, 05 Jun 2020 04:12:52 -0400
parents cb903c9dc33d
children db536ad45f28
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--- 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"/>