| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4 |
| toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3 |
| porechop |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| porechop | 0.2.4 | package |
| Additional information about this tool |
porechop
-i '$input_file'
--format '$format'
--barcode_threshold '$barcode_binning_settings.barcode_threshold'
--barcode_diff '$barcode_binning_settings.barcode_diff'
$barcode_binning_settings.require_two_barcodes
$barcode_binning_settings.discard_unassigned
--adapter_threshold '$adapter_search_settings.adapter_threshold'
--check_reads '$adapter_search_settings.check_reads'
--scoring_scheme '$adapter_search_settings.scoring_scheme'
--end_size '$end_adapter_settings.end_size'
--min_trim_size '$end_adapter_settings.min_trim_size'
--extra_end_trim '$end_adapter_settings.extra_end_trim'
--end_threshold '$end_adapter_settings.end_threshold'
$middle_adapter_settings.no_split
$middle_adapter_settings.discard_middle
--middle_threshold '$middle_adapter_settings.middle_threshold'
--extra_middle_trim_good_side '$middle_adapter_settings.extra_middle_trim_good_side'
--extra_middle_trim_bad_side '$middle_adapter_settings.extra_middle_trim_bad_side'
--min_split_read_size '$middle_adapter_settings.min_split_read_size'
-o 'out.$format'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_file: test_format.fasta format: fasta |
name: value |
test_format.fasta value |
| Test-2 |
input_file: test_format.fastq.gz format: fastq |
name: value |
test_format.fastq.gz value |
| Test-3 |
input_file: test_format.fastq.gz format: fastq |
name: value |
test_format.fastq.gz value |
| Test-4 |
input_file: test_format.fasta format: fasta.gz |
name: value |
test_format.fasta value |
| Test-5 |
input_file: test_format.fasta format: fastq.gz |
name: value |
test_format.fasta value |
| Test-6 |
input_file: test_format.fasta format: fasta barcode_binning_settings|barcode_threshold: 70 barcode_binning_settings|barcode_diff: 4 barcode_binning_settings|require_two_barcodes: True barcode_binning_settings|discard_unassigned: True end_adapter_settings|end_size: 100 end_adapter_settings|min_trim_size: 2 end_adapter_settings|extra_end_trim: 1 end_adapter_settings|end_threshold: 80 middle_adapter_settings|discard_middle: True middle_adapter_settings|middle_threshold: 90 middle_adapter_settings|min_split_read_size: 1500 |
name: value |
test_format.fasta value |