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comparison trimmomatic.xml @ 2:a60283899c6d draft

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Version 0.32.2: use GALAXY_SLOTS to set number of threads.
author pjbriggs
date Wed, 22 Apr 2015 09:36:27 -0400
parents 2bd7cdbb6228
children f8a9a5eaca8a
comparison
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1:2bd7cdbb6228 2:a60283899c6d
1 <tool id="trimmomatic" name="Trimmomatic" version="0.32.1"> 1 <tool id="trimmomatic" name="Trimmomatic" version="0.32.2">
2 <description>flexible read trimming tool for Illumina NGS data</description> 2 <description>flexible read trimming tool for Illumina NGS data</description>
3 <command interpreter="bash">trimmomatic.sh 3 <command interpreter="bash">trimmomatic.sh
4 -mx8G 4 -mx8G
5 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar 5 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar
6 #if $paired_end.is_paired_end 6 #if $paired_end.is_paired_end
7 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 7 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
8 #else 8 #else
9 SE -threads 6 -phred33 $fastq_in $fastq_out 9 SE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_in $fastq_out
10 #end if 10 #end if
11 ## ILLUMINACLIP option 11 ## ILLUMINACLIP option
12 #if $illuminaclip.do_illuminaclip 12 #if $illuminaclip.do_illuminaclip
13 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold 13 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
14 #end if 14 #end if