| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.9 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8 (this tool) |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.7 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.4 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.2 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.1 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.6 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.1.a |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/0.9.5.a |
| cutadapt |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| cutadapt | 1.16 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|input_1: cutadapt_small.fastq library|type: single library|r1|adapters_0|adapter_source|adapter_source_list: user |
attributes: name |
cutadapt_small.fastq name |
| Test-2 |
library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|input_1: bwa-mem-fastq1.fq.gz library|type: single library|r1|adapters_0|adapter_source|adapter_source_list: user |
attributes: name |
bwa-mem-fastq1.fq.gz name |
| Test-3 |
library|input_2: bwa-mem-fastq2.fq.gz library|input_1: bwa-mem-fastq1.fq.gz library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: paired library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source2|adapter_source_list2: user |
attributes: name attributes: name |
bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq.gz name |
| Test-4 |
library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|input_1: paired collection library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: paired_collection library|r2|adapters2_0|adapter_source2|adapter_source_list2: user |
attributes: name attributes: name |
bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq.gz name |
| Test-5 |
library|r1|adapters_0|adapter_source|adapter: TGTAGGCC library|input_1: cutadapt_small.fastq library|type: single library|r1|adapters_0|adapter_source|adapter_source_list: builtin |
attributes: name |
cutadapt_small.fastq name |
| Test-6 |
library|r1|adapters_0|adapter_source|adapter: TTAGACATATCTCCGTCG library|input_1: cutadapt_small.fastq filter_options|discard: True library|r1|adapters_0|adapter_source|adapter_source_list: user |
attributes: name |
cutadapt_small.fastq name |
| Test-7 |
library|r1|adapters_0|adapter_source|adapter: AAAGATG library|input_1: cutadapt_rest.fa output_options|rest_file: True library|r1|adapters_0|adapter_source|adapter_source_list: user |
attributes: name attributes: name |
cutadapt_rest.fa name |
| Test-8 |
read_mod_options|nextseq_trim: 20 library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|input_1: bwa-mem-fastq1.fq.gz library|type: single library|r1|adapters_0|adapter_source|adapter_source_list: user |
attributes: name |
bwa-mem-fastq1.fq.gz name |
| Test-9 |
library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter_source_list: user output_options|info_file: True library|type: single output_options|report: True |
attributes: name attributes: name attributes: name |
cutadapt_small.fastq name |
| Test-10 |
library|input_1: cutadapt_in_split.fastq library|r1|front_adapters_0|front_adapter_source|front_adapter: ^GTCGGTAA library|r1|front_adapters_0|front_adapter_source|front_adapter_name: A1 library|r1|front_adapters_0|front_adapter_source|front_adapter_source_list: user library|r1|front_adapters_1|front_adapter_source|front_adapter_name: A2 output_options|info_file: False library|type: single library|r1|front_adapters_1|front_adapter_source|front_adapter: ^AGGTCACT output_options|report: False output_options|multiple_output: True library|r1|front_adapters_1|front_adapter_source|front_adapter_source_list: user |
cutadapt_in_split.fastq |
|
| Test-11 |
library|input_1: cutadapt_in_split.fastq.gz output_options|multiple_output: True library|r1|front_adapters_0|front_adapter_source|front_adapter_source_list: file output_options|info_file: False library|type: single library|r1|front_adapters_0|front_adapter_source|front_adapter_file: barcodes.fasta output_options|report: False |
cutadapt_in_split.fastq.gz barcodes.fasta |
|
| Test-12 |
library|r1|adapters_0|adapter_source|adapter: AAAT library|input_1: cutadapt_small.fastq library|type: single library|r1|adapters_0|adapter_source|adapter_source_list: user output_options|untrimmed_file: True |
attributes: name attributes: name |
cutadapt_small.fastq name |
| Test-13 |
library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|input_1: bwa-mem-fastq1.fq.gz library|type: single library|r1|adapters_0|adapter_source|adapter_source_list: user output_options|untrimmed_file: True |
attributes: name attributes: name |
bwa-mem-fastq1.fq.gz name |
| Test-14 |
filter_options|max_n: 0 library|input_2: bwa-mem-fastq2.fq.gz library|input_1: bwa-mem-fastq1.fq.gz filter_options|discard_untrimmed: True library|type: paired library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source2|adapter_source_list2: user filter_options|min: 1 filter_options|max: 1000 filter_options|pair_filter: both |
bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq.gz |