| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.9 |
| toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8 |
| 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 | 3.4 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single |
name: value |
cutadapt_small.fastq value |
| Test-2 |
library|input_1: bwa-mem-fastq1.fq.gz library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single |
name: value |
bwa-mem-fastq1.fq.gz value |
| Test-3 |
library|input_1: bwa-mem-fastq1.fq.gz library|input_2: bwa-mem-fastq2.fq.gz library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source2|adapter_source_list2: user library|type: paired |
name: value name: value |
bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq.gz value |
| Test-4 |
library|input_1: paired collection library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source2|adapter_source_list2: user library|type: paired_collection |
bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq.gz |
|
| Test-5 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: TGTAGGCC library|r1|adapters_0|adapter_source|adapter_source_list: builtin library|type: single |
name: value |
cutadapt_small.fastq value |
| Test-6 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: TTAGACATATCTCCGTCG library|r1|adapters_0|adapter_source|adapter_source_list: user filter_options|discard_trimmed: True |
name: value |
cutadapt_small.fastq value |
| Test-7 |
library|input_1: cutadapt_rest.fa library|r1|adapters_0|adapter_source|adapter: AAAGATG library|r1|adapters_0|adapter_source|adapter_source_list: user output_selector: rest_file |
name: value name: value |
cutadapt_rest.fa value |
| Test-8 |
library|input_1: bwa-mem-fastq1.fq.gz library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single read_mod_options|nextseq_trim: 20 |
name: value |
bwa-mem-fastq1.fq.gz value |
| Test-9 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single output_selector: ['report', 'info_file'] |
name: value name: value name: value |
cutadapt_small.fastq value |
| Test-10 |
library|input_1: cutadapt_in_split.fastq library|r1|front_adapters_0|front_adapter_source|front_adapter_name: A1 library|r1|front_adapters_0|front_adapter_source|front_adapter: ^GTCGGTAA 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 library|r1|front_adapters_1|front_adapter_source|front_adapter: ^AGGTCACT library|r1|front_adapters_1|front_adapter_source|front_adapter_source_list: user library|type: single output_selector: multiple_output |
cutadapt_in_split.fastq |
|
| Test-11 |
library|input_1: cutadapt_in_split.fastq.gz library|r1|front_adapters_0|front_adapter_source|front_adapter_file: barcodes.fasta library|r1|front_adapters_0|front_adapter_source|front_adapter_source_list: file library|type: single output_selector: multiple_output |
cutadapt_in_split.fastq.gz barcodes.fasta |
|
| Test-12 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: AAAT library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single output_selector: untrimmed_file |
name: value name: value |
cutadapt_small.fastq value |
| Test-13 |
library|input_1: bwa-mem-fastq1.fq.gz library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single output_selector: untrimmed_file |
name: value name: value |
bwa-mem-fastq1.fq.gz value |
| Test-14 |
library|input_1: bwa-mem-fastq1.fq.gz library|input_2: bwa-mem-fastq2.fq.gz library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: paired filter_options|discard_untrimmed: True filter_options|maximum_length: 1000 filter_options|max_n: 0 filter_options|pair_filter: both |
bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq.gz |
|
| Test-15 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r1|cut: 5 library|type: single |
name: value |
cutadapt_small.fastq value |
| Test-16 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r1|cut: 5 library|type: single read_mod_options|rename: {id} barcode={cut_prefix} |
name: value |
cutadapt_small.fastq value |
| Test-17 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: CGTCCGAANTAG library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|action: retain |
name: value |
cutadapt_small.fastq value |
| Test-18 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: CGTCCGAANTAG library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|action: mask |
name: value |
cutadapt_small.fastq value |
| Test-19 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: CGTCCGAANTAG library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|action: lowercase |
name: value |
cutadapt_small.fastq value |
| Test-20 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: CGTCCGAANTAG library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|action: none |
name: value |
cutadapt_small.fastq value |
| Test-21 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: TAAACAGATTAGT library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|revcomp: True |
name: value |
cutadapt_small.fastq value |
| Test-22 |
library|input_1: bwa-mem-fastq1_assimetric.fq.gz library|input_2: bwa-mem-fastq2_assimetric.fq.gz library|r1|adapters_0|adapter_source|adapter: ATCTGGTTCC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r2|adapters2_0|adapter_source2|adapter2: CTACAAG library|r2|adapters2_0|adapter_source2|adapter_source_list2: user library|type: paired filter_options|minimum_length: 30 filter_options|length_R2_options|R2_minimum: 10 filter_options|length_R2_options|length_R2_status: True filter_options|pair_filter: both |
name: value name: value |
bwa-mem-fastq1_assimetric.fq.gz bwa-mem-fastq2_assimetric.fq.gz value |
| Test-23 |
library|input_1: bwa-mem-fastq1_assimetric.fq.gz library|input_2: bwa-mem-fastq2_assimetric.fq.gz library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source2|adapter_source_list2: user library|type: paired filter_options|maximum_length: 50 filter_options|length_R2_options|R2_maximum: 30 filter_options|length_R2_options|length_R2_status: True filter_options|pair_filter: both |
name: value name: value |
bwa-mem-fastq1_assimetric.fq.gz bwa-mem-fastq2_assimetric.fq.gz value |
| Test-24 |
library|input_1: bwa-mem-fastq1_assimetric.fq.gz library|input_2: bwa-mem-fastq2_assimetric.fq.gz library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source2|adapter_source_list2: user library|type: paired filter_options|minimum_length: 10 filter_options|maximum_length: 50 filter_options|length_R2_options|R2_maximum: 30 filter_options|length_R2_options|length_R2_status: True filter_options|pair_filter: both |
name: value name: value |
bwa-mem-fastq1_assimetric.fq.gz bwa-mem-fastq2_assimetric.fq.gz value |
| Test-25 |
library|input_1: bwa-mem-fastq1_assimetric.fq.gz library|input_2: bwa-mem-fastq2_assimetric.fq.gz library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source2|adapter_source_list2: user library|type: paired filter_options|minimum_length: 10 filter_options|maximum_length: 50 filter_options|length_R2_options|R2_minimum: 10 filter_options|length_R2_options|length_R2_status: True filter_options|pair_filter: both |
name: value name: value |
bwa-mem-fastq1_assimetric.fq.gz bwa-mem-fastq2_assimetric.fq.gz value |
| Test-26 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: AGCCGCTANGACG library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single read_mod_options|shorten_options|length: 10 read_mod_options|shorten_options|shorten_end: 3prime read_mod_options|shorten_options|shorten_values: True |
name: value |
cutadapt_small.fastq value |
| Test-27 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: AGCCGCTANGACG library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single read_mod_options|shorten_options|length: 10 read_mod_options|shorten_options|shorten_end: 5prime read_mod_options|shorten_options|shorten_values: True |
name: value |
cutadapt_small.fastq value |
| Test-28 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: AGCGGCTTAGACG library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single filter_options|max_expected_errors: 10 |
name: value |
cutadapt_small.fastq value |
| Test-29 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: GAANTAGCTACCAC library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|internal: X |
name: value |
cutadapt_small.fastq value |
| Test-30 |
library|input_1: bwa-mem-fastq1_assimetric.fq.gz library|input_2: bwa-mem-fastq2_assimetric.fq.gz library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r2|adapters2_0|adapter_source2|adapter2: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source2|adapter_source_list2: user library|type: paired adapter_options|internal: X |
name: value name: value |
bwa-mem-fastq1_assimetric.fq.gz bwa-mem-fastq2_assimetric.fq.gz value |
| Test-31 |
library|input_1: cutadapt_small.fastq library|r1|adapters_0|adapter_source|adapter: TGTAGGCC library|r1|adapters_0|adapter_source|adapter_source_list: builtin library|type: single adapter_options|internal: X |
name: value |
cutadapt_small.fastq value |