Mercurial > repos > pjbriggs > trimmomatic

diff trimmomatic.xml @ 2:e7c8359dfa23 draft

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Uploaded version 0.32.2 (now uses GALAXY_SLOTS).
author pjbriggs
date Wed, 22 Apr 2015 09:28:59 -0400
parents a2e6088d1165
children a7139c612c45
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--- a/trimmomatic.xml	Thu Mar 19 06:13:35 2015 -0400
+++ b/trimmomatic.xml	Wed Apr 22 09:28:59 2015 -0400
@@ -1,12 +1,12 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.32.1">
+<tool id="trimmomatic" name="Trimmomatic" version="0.32.2">
   <description>flexible read trimming tool for Illumina NGS data</description>
   <command interpreter="bash">trimmomatic.sh
   -mx8G
   -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar
   #if $paired_end.is_paired_end
-    PE -threads 6 -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired 
+    PE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired 
   #else
-    SE -threads 6 -phred33 $fastq_in $fastq_out
+    SE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_in $fastq_out
   #end if
   ## ILLUMINACLIP option
   #if $illuminaclip.do_illuminaclip