Mercurial > repos > iuc > ivar_trim

diff ivar_trim.xml @ 3:f78f33bdfce1 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 08:03:23 +0000
parents 9ebf6615d8f7
children 3c20a5cc3914
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--- a/ivar_trim.xml	Wed Apr 22 10:01:06 2020 +0000
+++ b/ivar_trim.xml	Fri Jun 05 08:03:23 2020 +0000
@@ -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"/>