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
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