| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.2.3 (this tool) |
| toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.2.2 |
| toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.2.1 |
| toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.2.0 |
| toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.1.1 |
| toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5 |
| toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.3 |
| toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.2 |
| toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.1 |
| get_orfs_or_cdss |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| biopython | 1.67 | package |
| Additional information about this tool |
python $__tool_directory__/get_orfs_or_cdss.py
-i '$input_file'
-f '$input_file.ext'
--table '$table'
-t '$ftype'
-e '$ends'
-m '$mode'
--min_len '$min_len'
-s '$strand'
--on '$out_nuc_file'
--op '$out_prot_file'
--ob '$out_bed_file'
--og '$out_gff3_file'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_file: get_orf_input.fasta table: 1 ftype: CDS ends: open mode: all min_len: 10 strand: forward |
name: value name: value name: value name: value |
get_orf_input.fasta value |
| Test-2 |
input_file: get_orf_input.fasta table: 11 ftype: CDS ends: closed mode: all min_len: 10 strand: forward |
name: value name: value name: value name: value |
get_orf_input.fasta value |
| Test-3 |
input_file: get_orf_input.fasta table: 11 ftype: CDS ends: open mode: all min_len: 10 strand: forward |
name: value name: value name: value name: value |
get_orf_input.fasta value |
| Test-4 |
input_file: Ssuis.fasta table: 11 ftype: ORF ends: open mode: all min_len: 100 strand: both |
name: value name: value name: value name: value |
Ssuis.fasta value |