Workflow: prok-annotation-cheetah.cwl
Fetched 2024-04-23 05:52:17 GMT
Verified with cwltool version 3.1.20221201130942
- 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
