Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.7+galaxy0 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy2 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy0 |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy2 |
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 | 4.8 | 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_source|adapter: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source|adapter_source_list: 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_source|adapter: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source|adapter_source_list: 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', 'json_stats'] |
name: value 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|adapter_source|adapter_name: A1 library|r1|front_adapters_0|adapter_source|adapter: ^GTCGGTAA library|r1|front_adapters_0|adapter_source|adapter_source_list: user library|r1|front_adapters_1|adapter_source|adapter_name: A2 library|r1|front_adapters_1|adapter_source|adapter: ^AGGTCACT library|r1|front_adapters_1|adapter_source|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|adapter_source|adapter_file: barcodes.fasta library|r1|front_adapters_0|adapter_source|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|type: single read_mod_options|cut: 5 |
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|type: single read_mod_options|cut: 5 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_source|adapter: CTACAAG library|r2|adapters2_0|adapter_source|adapter_source_list: user library|r2|minimum_length2: 10 library|type: paired filter_options|minimum_length: 30 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_source|adapter: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source|adapter_source_list: user library|r2|maximum_length2: 30 library|type: paired filter_options|maximum_length: 50 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|maximum_length2: 30 library|type: paired filter_options|minimum_length: 10 filter_options|maximum_length: 50 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|minimum_length2: 10 library|type: paired filter_options|minimum_length: 10 filter_options|maximum_length: 50 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: GAANTAGCTACCACX library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single |
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: AGATCGGAAGAGCX library|r1|adapters_0|adapter_source|adapter_source_list: user library|r2|adapters2_0|adapter_source|adapter: AGATCGGAAGAGCX library|r2|adapters2_0|adapter_source|adapter_source_list: user library|type: paired |
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 |
name: value |
cutadapt_small.fastq value |
Test-32 |
library|input_1: paired collection library|r1|adapters_0|adapter_source|adapter: AGATCGGAAGAGC library|r1|adapters_0|adapter_source|adapter_source_list: user library|r1|adapters_0|single_noindels: True library|r2|adapters2_0|adapter_source|adapter: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source|adapter_source_list: user library|r2|adapters2_0|single_noindels: True library|type: paired_collection |
bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq.gz |
|
Test-33 |
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_source|adapter: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source|adapter_source_list: user library|r2|quality_cutoff2: 15,20 library|type: paired_collection read_mod_options|quality_cutoff: 5 |
bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq.gz |
|
Test-34 |
library|input_1: paired collection library|type: paired_collection read_mod_options|poly_a: True |
cutadapt/data/polya.1.fasta cutadapt/data/polya.2.fasta |
|
Test-35 |
library|input_1: cutadapt/data/polya.1.fasta library|r1|adapters_0|adapter_source|adapter: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|overlap: 10 |
name: value |
cutadapt/data/polya.1.fasta value |
Test-36 |
library|input_1: cutadapt/data/polya.1.fasta library|r1|adapters_0|adapter_source|adapter: A{35} library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|overlap: 10 |
name: value |
cutadapt/data/polya.1.fasta value |
Test-37 |
library|input_1: cutadapt/data/polya.1.fasta library|type: single read_mod_options|poly_a: True |
name: value |
cutadapt/data/polya.1.fasta value |
Test-38 |
library|input_1: cutadapt/data/simple.fasta.gz library|type: single |
name: value |
cutadapt/data/simple.fasta.gz value |
Test-39 |
library|input_1: cutadapt/data/illumina64.fastq library|r1|adapters_0|adapter_source|adapter: XXXXXX library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single read_mod_options|quality_cutoff: 10 |
name: value |
cutadapt/data/illumina64.fastq value |
Test-40 |
library|input_1: cutadapt/data/illumina64.fastq library|type: single read_mod_options|quality_cutoff: 10 |
name: value |
cutadapt/data/illumina64.fastq value |
Test-41 |
library|input_1: cutadapt/data/maxee.fastq library|type: single filter_options|max_expected_errors: 0.9 output_selector: ['report', 'info_file'] |
name: value name: value name: value |
cutadapt/data/maxee.fastq value |
Test-42 |
library|input_1: cutadapt/data/wildcard.fa library|r1|anywhere_adapters_0|adapter_source|adapter: ACGTACGT library|r1|anywhere_adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|match_read_wildcards: True |
name: value |
cutadapt/data/wildcard.fa value |
Test-43 |
library|input_1: cutadapt/data/wildcardN.fa library|r1|adapters_0|adapter_source|adapter: GGGGGGG library|r1|adapters_0|adapter_source|adapter_source_list: user library|type: single adapter_options|error_rate: 0 adapter_options|match_read_wildcards: True |
name: value |
cutadapt/data/wildcardN.fa value |
Test-44 |
library|input_1: bwa-mem-fastq1.fq.gz library|input_2: bwa-mem-fastq_mispaired2.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_source|adapter: AGATCGGAAGAGC library|r2|adapters2_0|adapter_source|adapter_source_list: user library|type: paired |
bwa-mem-fastq1.fq.gz bwa-mem-fastq_mispaired2.fq.gz |