Repository revision
17:b9aaed85cbd1

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/0.39+galaxy2
0.39+galaxy2
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2 (this tool)
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy1
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy0
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.6
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 0.39 package
coreutils 9.4 package
Functional tests
name inputs outputs required files
Test-1 readtype|fastq_in: Illumina_SG_R1.fastq
readtype|single_or_paired: se
operations_0|operation|name: SLIDINGWINDOW
output_logs: True
output_err: True
name: value
name: value
name: value
Illumina_SG_R1.fastq
value
Test-2 readtype|fastq_in: Illumina_SG_R1.fastq.gz
readtype|single_or_paired: se
operations_0|operation|name: SLIDINGWINDOW
name: value
Illumina_SG_R1.fastq.gz
value
Test-3 readtype|fastq_r1_in: Illumina_SG_R1.fastq.gz
readtype|fastq_r2_in: Illumina_SG_R2.fastq.gz
readtype|single_or_paired: pair_of_files
operations_0|operation|name: SLIDINGWINDOW
name: value
name: value
name: value
name: value
Illumina_SG_R1.fastq.gz
Illumina_SG_R2.fastq.gz
value
Test-4 readtype|fastq_r1_in: Illumina_SG_R1.fastq
readtype|fastq_r2_in: Illumina_SG_R2.fastq
readtype|single_or_paired: pair_of_files
operations_0|operation|name: SLIDINGWINDOW
name: value
name: value
name: value
name: value
Illumina_SG_R1.fastq
Illumina_SG_R2.fastq
value
Test-5 readtype|fastq_r1_in: Illumina_SG_R1.fastqillumina
readtype|fastq_r2_in: Illumina_SG_R2.fastqillumina
readtype|single_or_paired: pair_of_files
operations_0|operation|name: SLIDINGWINDOW
name: value
name: value
name: value
name: value
Illumina_SG_R1.fastqillumina
Illumina_SG_R2.fastqillumina
value
Test-6 readtype|fastq_r1_in: Illumina_SG_R1.fastqsolexa
readtype|fastq_r2_in: Illumina_SG_R2.fastqsolexa
readtype|single_or_paired: pair_of_files
operations_0|operation|name: SLIDINGWINDOW
name: value
name: value
name: value
name: value
Illumina_SG_R1.fastqsolexa
Illumina_SG_R2.fastqsolexa
value
Test-7 readtype|fastq_in: Illumina_SG_R1.fastq
readtype|single_or_paired: se
operations_0|operation|crop: 10
operations_0|operation|name: CROP
name: value
Illumina_SG_R1.fastq
value
Test-8 readtype|fastq_pair: paired collection
readtype|single_or_paired: collection
operations_0|operation|name: SLIDINGWINDOW
Illumina_SG_R1.fastq
Illumina_SG_R2.fastq
Test-9 readtype|fastq_pair: paired collection
readtype|single_or_paired: collection
operations_0|operation|name: SLIDINGWINDOW
Illumina_SG_R1.fastq.gz
Illumina_SG_R2.fastq.gz
Test-10 readtype|fastq_in: Illumina_SG_R1.fastq
readtype|single_or_paired: se
operations_0|operation|avgqual: 30
operations_0|operation|name: AVGQUAL
name: value
Illumina_SG_R1.fastq
value
Test-11 readtype|fastq_in: Illumina_SG_R1.fastq
readtype|single_or_paired: se
operations_0|operation|target_length: 75
operations_0|operation|strictness: 0.8
operations_0|operation|name: MAXINFO
name: value
Illumina_SG_R1.fastq
value
Test-12 readtype|fastq_r1_in: Illumina_SG_R1.fastq
readtype|fastq_r2_in: Illumina_SG_R2.fastq
readtype|single_or_paired: pair_of_files
illuminaclip|adapter_type|adapter_fasta: TruSeq2-PE.fa
illuminaclip|do_illuminaclip: yes
operations_0|operation|name: SLIDINGWINDOW
name: value
name: value
name: value
name: value
Illumina_SG_R1.fastq
Illumina_SG_R2.fastq
value
Test-13 readtype|fastq_r1_in: Illumina_SG_R1.fastq
readtype|fastq_r2_in: Illumina_SG_R2.fastq
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|adapter_type|standard_or_custom: custom
illuminaclip|do_illuminaclip: yes
operations_0|operation|name: SLIDINGWINDOW
name: value
name: value
name: value
name: value
Illumina_SG_R1.fastq
Illumina_SG_R2.fastq
value
Test-14 readtype|fastq_in: Illumina_SG_R1.fastq
readtype|single_or_paired: se
operations_0|operation|name: SLIDINGWINDOW
quality_score: -phred33
output_logs: True
output_err: True
name: value
name: value
name: value
Illumina_SG_R1.fastq
value