Mercurial > repos > drosofff > msp_sr_bowtie

changeset 30:5bd8c555390d draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty
author drosofff
date Sun, 02 Jul 2017 12:40:56 -0400
parents 04685a1b3de1
children e0a3a72719f3
files sRbowtie.xml
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/sRbowtie.xml	Sun Jul 02 12:34:18 2017 -0400
+++ b/sRbowtie.xml	Sun Jul 02 12:40:56 2017 -0400
@@ -46,11 +46,11 @@
 
         ## run the bowtie alignement
         #if $output_format == "tabular":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > '$output'
+            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > $output
         #elif $output_format == "sam":
             bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output'
         #elif $output_format == "bam":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o '$output'
+            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o $output
         #end if
         ##### | samtools view -uS
         ]]></command>