Repository revision
9:1bfc7254232e

Repository 'trim_galore'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore

Trim Galore! tool metadata
Miscellaneous
Trim Galore!
Quality and adapter trimmer of reads
trim_galore
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2
0.4.2
perl $__tool_directory__/trim_galore --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.1
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.0
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.3.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.2.8.1
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.2.8
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.2.4.1
trim_galore
Requirements (dependencies defined in the <requirements> tag set)
name version type
cutadapt 1.8.3 package
cutadapt 1.8 package
Functional tests
name inputs outputs required files
Test-1 params|report: True
params|settingsType: custom
singlePaired|sPaired: single
singlePaired|input_singles: sanger_full_range_original_sanger.fastqsanger
trimmed_reads_single: sanger_full_range_results1.fastqsanger
report_file: sanger_full_range_report_results1.txt
sanger_full_range_original_sanger.fastqsanger
sanger_full_range_results1.fastqsanger
sanger_full_range_report_results1.txt
Test-2 singlePaired|trimming|trimming_select: --illumina
singlePaired|sPaired: single
singlePaired|input_singles: sanger_full_range_original_sanger.fastqsanger
trimmed_reads_single: sanger_full_range_results2.fastqsanger
sanger_full_range_original_sanger.fastqsanger
sanger_full_range_results2.fastqsanger
Test-3 singlePaired|sPaired: single
singlePaired|input_singles: sanger_full_range_original_sanger.fastqsanger
trimmed_reads_single: sanger_full_range_results3.fastqsanger
sanger_full_range_original_sanger.fastqsanger
sanger_full_range_results3.fastqsanger
Test-4 params|report: True
singlePaired|input_mate2: bwa-mem-fastq2.fq
singlePaired|input_mate1: bwa-mem-fastq1.fq
params|settingsType: custom
singlePaired|sPaired: paired
trimmed_reads_pair1: paired_example_pair1_results2.fastqsanger
trimmed_reads_pair2: paired_example_pair2_results2.fastqsanger
report_file: paired_example_results2.txt
bwa-mem-fastq1.fq
bwa-mem-fastq2.fq
paired_example_pair1_results2.fastqsanger
paired_example_pair2_results2.fastqsanger
paired_example_results2.txt
Test-5 params|report: True
params|settingsType: custom
params|retain_unpaired|retain_unpaired_select: retain_unpaired_output
singlePaired|input_mate_pairs: paired collection
singlePaired|sPaired: paired_collection
report_file: paired_collection_example_results3.txt
bwa-mem-fastq1.fq
bwa-mem-fastq2.fq
paired_collection_example_results3.txt