Mercurial > repos > pjbriggs > trimmomatic

comparison trimmomatic.xml @ 2:e7c8359dfa23 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded version 0.32.2 (now uses GALAXY_SLOTS).
author pjbriggs
date Wed, 22 Apr 2015 09:28:59 -0400
parents a2e6088d1165
children a7139c612c45
comparison
equal deleted inserted replaced
1:a2e6088d1165 2:e7c8359dfa23
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