| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/abims-sbr/cds_search/cds_search/2.2.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/abims-sbr/cds_search/cds_search/2.1.2 |
| cds_search |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| biopython | 1.79 | package |
| Additional information about this tool |
#for $input in $inputs
ln -s '$input' '$input.element_identifier';
echo '$input.element_identifier' >> list_files;
#end for
ln -s $__tool_directory__/scripts/dico.py . &&
python $__tool_directory__/scripts/S01_find_orf_on_multiple_alignment.py
$__tool_directory__/scripts/code_universel_modified.txt
$length.min_length_seq
$nb_species_keep
list_files
> '$log' &&
python $__tool_directory__/scripts/S02_remove_too_short_bit_or_whole_sequence.py
$nb_species_keep
$methionine
$length.min_length_seq
$length.min_length_subseq
>> '$log' &&
python $__tool_directory__/scripts/S03_remove_site_with_not_enough_species_represented.py
$nb_species_keep
$length.min_length_nuc
>> '$log';
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputs: ['inputs/orthogroup_1_with_4_sequences.fasta', 'inputs/orthogroup_6_with_4_sequences.fasta', 'inputs/orthogroup_7_with_3_sequences.fasta', 'inputs/orthogroup_8_with_4_sequences.fasta', 'inputs/orthogroup_12_with_5_sequences.fasta', 'inputs/orthogroup_14_with_4_sequences.fasta'] nb_species_keep: 3 methionine: False length|min_length_seq: 50 length|min_length_subseq: 15 length|min_length_nuc: 50 out_BESTORF: both out_CDS: both out_CDS_filter: both |
inputs/orthogroup_1_with_4_sequences.fasta inputs/orthogroup_6_with_4_sequences.fasta inputs/orthogroup_7_with_3_sequences.fasta inputs/orthogroup_8_with_4_sequences.fasta inputs/orthogroup_12_with_5_sequences.fasta inputs/orthogroup_14_with_4_sequences.fasta |
|
| Test-2 |
inputs: ['inputs/orthogroup_1_with_4_sequences.fasta', 'inputs/orthogroup_6_with_4_sequences.fasta', 'inputs/orthogroup_7_with_3_sequences.fasta', 'inputs/orthogroup_8_with_4_sequences.fasta', 'inputs/orthogroup_12_with_5_sequences.fasta', 'inputs/orthogroup_14_with_4_sequences.fasta'] nb_species_keep: 2 methionine: True length|min_length_seq: 50 length|min_length_subseq: 15 length|min_length_nuc: 50 out_BESTORF: both out_CDS: both out_CDS_filter: both |
inputs/orthogroup_1_with_4_sequences.fasta inputs/orthogroup_6_with_4_sequences.fasta inputs/orthogroup_7_with_3_sequences.fasta inputs/orthogroup_8_with_4_sequences.fasta inputs/orthogroup_12_with_5_sequences.fasta inputs/orthogroup_14_with_4_sequences.fasta |