- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
out_dir | String |
Location where split files will be written |
|
source_fasta | File |
Starting protein multi-FASTA file |
|
output_format | String |
Prodigal prediction output format |
|
aragorn_format | Boolean | ||
hmmscan_threads | Integer | ||
tmhmm_input_file | File | ||
hmmscan_query_file | File | ||
rapsearch2_threads | Integer | ||
fragmentation_count | Integer |
How many files the input will be split into |
|
hmmscan_output_file | String | ||
initial_protein_out | String |
Prodigal polypeptide FASTA prediction file |
|
prodigal2fasta_type | String | ||
raw2htab_input_file | File | ||
raw2htab_mldbm_file | File | ||
prodigal2fasta_fasta | File |
Genomic FASTA |
|
raw2htab_output_htab | String | ||
barrnap_genomic_fasta | File |
Input genomic FASTA file |
|
hmmscan_database_file | File | ||
rapsearch2_query_file | File | ||
attributor_config_file | String | ||
attributor_output_base | String | ||
attributor_source_gff3 | File | ||
hmmscan_use_accessions | Boolean | ||
attributor_output_format | String | ||
hmmscan_cutoff_gathering | Boolean | ||
prodigal2gff3_input_file | File | ||
rapsearch2_database_file | File | ||
prodigal2fasta_input_file | File | ||
prodigal2gff3_output_file | String | ||
prodigal2fasta_output_file | String | ||
prodigal2fasta_feature_type | String | ||
rapsearch2_output_file_base | String | ||
attributor_polypeptide_fasta | File | ||
initial_structural_prediction | String |
Prodigal structural prediction file |
|
rapsearch2_one_line_desc_count | Integer |
Number of matches to return |
|
attributor_hmm_attribute_lookup_file | File | ||
attributor_blast_attribute_lookup_file | File |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
tmhmm |
../tools/tmhmm.cwl
(CommandLineTool)
|
||
aragorn |
../tools/aragorn.cwl
(CommandLineTool)
|
||
barrnap |
../tools/barrnap.cwl
(CommandLineTool)
|
||
hmmscan |
../tools/hmmer3-hmmscan.cwl
(CommandLineTool)
|
||
prodigal |
../tools/prodigal.cwl
(CommandLineTool)
|
||
raw2htab |
../tools/biocode-ConvertHmmscanToHtab.cwl
(CommandLineTool)
|
||
attributor |
../tools/attributor-prok-cheetah.cwl
(CommandLineTool)
|
||
rapsearch2 |
../tools/rapsearch2.cwl
(CommandLineTool)
|
||
prodigal2gff3 |
../tools/biocode-ConvertProdigalToGFF3.cwl
(CommandLineTool)
|
||
prodigal2fasta |
../tools/biocode-WriteFastaFromGFF.cwl
(CommandLineTool)
|
||
split_multifasta |
../tools/biocode-SplitFastaIntoEvenFiles.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
fasta_files | File[] | ||
prodigal_gff3 | File | ||
tmhmm_raw_files | File[] | ||
attributor_files | File[] | ||
hmmscan_raw_files | File[] | ||
aragorn_raw_output | File | ||
barrnap_gff_output | File | ||
hmmscan_htab_files | File[] | ||
prodigal_annot_file | File | ||
rapsearch2_m8_files | File[] | ||
prodigal_protein_file | File | ||
prodigal_protein_fasta | File | ||
attributor_output_config | File |
Permalink:
https://w3id.org/cwl/view/git/f4faa8acf34fba5e2ef746ab4302cbe6f8f6b083/cwl/workflows/prok-annotation-cheetah.cwl