Mercurial > repos > drosofff > msp_sr_bowtie

diff sRbowtie.xml @ 25:592eab0f31ac draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 5eaa99265d9ab0f4a2fbe25040c8a1e53fb82b39
author drosofff
date Fri, 30 Jun 2017 18:12:45 -0400
parents 2f4e22f2177d
children 405cd77e5a83
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--- a/sRbowtie.xml	Wed Jun 28 17:45:25 2017 -0400
+++ b/sRbowtie.xml	Fri Jun 30 18:12:45 2017 -0400
@@ -50,7 +50,7 @@
         #elif $output_format == "sam":
             bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input > $output
         #elif $output_format == "bam":
-            bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input | samtools sort -O bam -o '$output'
+            bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input | samtools view -uS | samtools sort -O bam -o '$output'
         #end if
         
         ]]></command>