Repository revision
12:51b771646466

Repository 'trimmomatic'
hg clone https://toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic

Trimmomatic tool metadata
Miscellaneous
Trimmomatic
flexible read trimming tool for Illumina NGS data
trimmomatic
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.6
0.36.6
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.6 (this tool)
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.4
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.3
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.2
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.1
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.0
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.2
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.1
trimmomatic
Requirements (dependencies defined in the <requirements> tag set)
name version type
trimmomatic 0.36 package
Additional information about this tool
if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi &&
  if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi &&
  #if $readtype.single_or_paired == "pair_of_files"
    #set r1_ext = $readtype.fastq_r1_in.extension
    #set r2_ext = $readtype.fastq_r2_in.extension
    ln -s '$readtype.fastq_r1_in' fastq_r1.'$r1_ext' &&
    ln -s '$readtype.fastq_r2_in' fastq_r2.'$r2_ext' &&
  #elif $readtype.single_or_paired == "collection"
    #set r1_ext = $readtype.fastq_pair.forward.extension
    #set r2_ext = $readtype.fastq_pair.reverse.extension
    ln -s '$readtype.fastq_pair.forward' fastq_r1.'$r1_ext' &&
    ln -s '$readtype.fastq_pair.reverse' fastq_r2.'$r2_ext' &&
  #else
    ln -s '$fastq_in' fastq_in.'$fastq_in.extension' &&
  #end if
  java \${_JAVA_OPTIONS:--Xmx8G} -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
  #if $readtype.single_or_paired in ["pair_of_files","collection"]
    PE -threads \${GALAXY_SLOTS:-6}
      fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
      fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
      fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
  #else
    SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
  #end if
  ## ILLUMINACLIP option
  #if $illuminaclip.do_illuminaclip
    #if $illuminaclip.adapter_type.standard_or_custom == "custom"
      #if $readtype.single_or_paired in ["pair_of_files","collection"]
        ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads
      #else
        ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
      #end if
    #else
      #if $readtype.single_or_paired in ["pair_of_files","collection"]
        ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads
      #else
        ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
      #end if
    #end if
  #end if
  ## Other operations
  #for $op in $operations
    ## SLIDINGWINDOW
    #if str( $op.operation.name ) == "SLIDINGWINDOW"
      SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality
    #end if
    ## MINLEN:36
    #if str( $op.operation.name ) == "MINLEN"
      MINLEN:$op.operation.minlen
    #end if
    #if str( $op.operation.name ) == "LEADING"
      LEADING:$op.operation.leading
    #end if
    #if str( $op.operation.name ) == "TRAILING"
      TRAILING:$op.operation.trailing
    #end if
    #if str( $op.operation.name ) == "CROP"
      CROP:$op.operation.crop
    #end if
    #if str( $op.operation.name ) == "HEADCROP"
      HEADCROP:$op.operation.headcrop
    #end if
    #if str( $op.operation.name ) == "AVGQUAL"
      AVGQUAL:$op.operation.avgqual
    #end if
    #if str( $op.operation.name ) == "MAXINFO"
      MAXINFO:$op.operation.target_length:$op.operation.strictness
    #end if
  #end for
  #if $output_logs:
    -trimlog trimlog
  #end if
  2>&1 | tee trimmomatic.log &&
  if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
  &&
  #if $readtype.single_or_paired  == "pair_of_files"
    mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
    mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
    mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
    mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
  #elif $readtype.single_or_paired  == "collection"
    mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
    mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
    mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
    mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
  #else
    mv fastq_out.'$fastq_in.extension' '${fastq_out}'
  #end if
  
None
False
False
Functional tests
name inputs outputs required files
Test-1 readtype|single_or_paired: se
readtype|fastq_in: Illumina_SG_R1.fastq
output_logs: True
operations_0|operation|name: SLIDINGWINDOW
output_err: True
attributes: name
attributes: name
attributes: name
Illumina_SG_R1.fastq
name
Test-2 readtype|single_or_paired: se
readtype|fastq_in: Illumina_SG_R1.fastq.gz
operations_0|operation|name: SLIDINGWINDOW
attributes: name
Illumina_SG_R1.fastq.gz
name
Test-3 readtype|fastq_r2_in: Illumina_SG_R2.fastq.gz
readtype|fastq_r1_in: Illumina_SG_R1.fastq.gz
operations_0|operation|name: SLIDINGWINDOW
readtype|single_or_paired: pair_of_files
attributes: name
attributes: name
attributes: name
attributes: name
Illumina_SG_R1.fastq.gz
Illumina_SG_R2.fastq.gz
name
Test-4 readtype|fastq_r2_in: Illumina_SG_R2.fastq
readtype|fastq_r1_in: Illumina_SG_R1.fastq
operations_0|operation|name: SLIDINGWINDOW
readtype|single_or_paired: pair_of_files
attributes: name
attributes: name
attributes: name
attributes: name
Illumina_SG_R1.fastq
Illumina_SG_R2.fastq
name
Test-5 readtype|fastq_r2_in: Illumina_SG_R2.fastqillumina
readtype|fastq_r1_in: Illumina_SG_R1.fastqillumina
operations_0|operation|name: SLIDINGWINDOW
readtype|single_or_paired: pair_of_files
attributes: name
attributes: name
attributes: name
attributes: name
Illumina_SG_R1.fastqillumina
Illumina_SG_R2.fastqillumina
name
Test-6 readtype|fastq_r2_in: Illumina_SG_R2.fastqsolexa
readtype|fastq_r1_in: Illumina_SG_R1.fastqsolexa
operations_0|operation|name: SLIDINGWINDOW
readtype|single_or_paired: pair_of_files
attributes: name
attributes: name
attributes: name
attributes: name
Illumina_SG_R1.fastqsolexa
Illumina_SG_R2.fastqsolexa
name
Test-7 readtype|single_or_paired: se
readtype|fastq_in: Illumina_SG_R1.fastq
operations_0|operation|name: CROP
operations_0|operation|crop: 10
attributes: name
Illumina_SG_R1.fastq
name
Test-8 readtype|fastq_pair: paired collection
operations_0|operation|name: SLIDINGWINDOW
readtype|single_or_paired: collection
Illumina_SG_R1.fastq
Illumina_SG_R2.fastq
Test-9 readtype|fastq_pair: paired collection
operations_0|operation|name: SLIDINGWINDOW
readtype|single_or_paired: collection
Illumina_SG_R1.fastq.gz
Illumina_SG_R2.fastq.gz
Test-10 readtype|single_or_paired: se
readtype|fastq_in: Illumina_SG_R1.fastq
operations_0|operation|avgqual: 30
operations_0|operation|name: AVGQUAL
attributes: name
Illumina_SG_R1.fastq
name
Test-11 readtype|single_or_paired: se
readtype|fastq_in: Illumina_SG_R1.fastq
operations_0|operation|name: MAXINFO
operations_0|operation|target_length: 75
operations_0|operation|strictness: 0.8
attributes: name
Illumina_SG_R1.fastq
name
Test-12 readtype|single_or_paired: pair_of_files
illuminaclip|adapter_type|adapter_fasta: TruSeq2-PE.fa
illuminaclip|do_illuminaclip: True
readtype|fastq_r2_in: Illumina_SG_R2.fastq
readtype|fastq_r1_in: Illumina_SG_R1.fastq
operations_0|operation|name: SLIDINGWINDOW
attributes: name
attributes: name
attributes: name
attributes: name
Illumina_SG_R1.fastq
Illumina_SG_R2.fastq
name
Test-13 illuminaclip|adapter_type|standard_or_custom: custom
readtype|single_or_paired: pair_of_files
illuminaclip|adapter_type|adapter_text: >PrefixPE/1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PrefixPE/2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PCR_Primer1_rc AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT >PCR_Primer2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer2_rc AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG >FlowCell1 TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC >FlowCell2 TTTTTTTTTTCAAGCAGAAGACGGCATACGA
illuminaclip|do_illuminaclip: True
readtype|fastq_r2_in: Illumina_SG_R2.fastq
readtype|fastq_r1_in: Illumina_SG_R1.fastq
operations_0|operation|name: SLIDINGWINDOW
attributes: name
attributes: name
attributes: name
attributes: name
Illumina_SG_R1.fastq
Illumina_SG_R2.fastq
name