| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.1 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16 (this tool) |
| 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 |
out1: cutadapt_small.out |
cutadapt_small.fastq cutadapt_small.out |
| 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 |
out1: cutadapt_out1.fq.gz |
bwa-mem-fastq1.fq.gz cutadapt_out1.fq.gz |
| Test-3 |
library|input_2: bwa-mem-fastq2.fq.gz library|input_1: bwa-mem-fastq1.fq.gz library|type: paired library|r2|adapters2_0|adapter_source2|adapter_source_list2: user library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user |
out1: cutadapt_out1.fq.gz out2: cutadapt_out2.fq.gz |
bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq.gz cutadapt_out1.fq.gz cutadapt_out2.fq.gz |
| Test-4 |
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 |
out1: cutadapt_builtin.out |
cutadapt_small.fastq cutadapt_builtin.out |
| Test-5 |
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 |
out1: cutadapt_discard.out |
cutadapt_small.fastq cutadapt_discard.out |
| Test-6 |
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 |
out1: cutadapt_rest.out rest_output: cutadapt_rest2.out |
cutadapt_rest.fa cutadapt_rest.out cutadapt_rest2.out |
| Test-7 |
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 |
out1: cutadapt_nextseq_out.fq.gz |
bwa-mem-fastq1.fq.gz cutadapt_nextseq_out.fq.gz |
| Test-8 |
library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|input_1: cutadapt_small.fastq library|type: single output_options|info_file: True library|r1|adapters_0|adapter_source|adapter_source_list: user output_options|report: True |
out1: cutadapt_small.out report: None info_file: cutadapt_info_out.txt |
cutadapt_small.fastq cutadapt_small.out cutadapt_info_out.txt |