Workflow: foldseek easy-search sub-workflow
Fetched 2024-11-20 06:50:22 GMT
Verified with cwltool version 3.1.20230201224320
retrieve sequence from blastdbcmd result makeblastdb: ../Tools/14_makeblastdb.cwl blastdbcmd: ../Tools/15_blastdbcmd.cwl seqretsplit: ../Tools/16_seqretsplit.cwl needle (Global alignment): ../Tools/17_needle.cwl water (Local alignment): ../Tools/17_water.cwl
- 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 |
|---|---|---|---|
| PARAM_FOLDSEEK_EXTRACT_TSV | File [TSV] |
foldseek extract tsv |
|
| PARAM_WATER_RESULT_DIR_NAME | String |
water result directory name |
|
| PARAM_NEEDLE_RESULT_DIR_NAME | String |
needle result directory name |
|
| PARAM_ALIGNMENT_QUERY_COL_NUM | Integer |
alignment query column number |
|
| PARAM_ENTRY_BATCH_HIT_SPECIES | File |
entry batch file |
|
| PARAM_ALIGNMENT_TARGET_COL_NUM | Integer |
alignment target column number |
|
| PARAM_LOGFILE_NAME_HIT_SPECIES | String |
logfile name |
|
| PARAM_ENTRY_BATCH_QUERY_SPECIES | File |
entry batch file |
|
| PARAM_INDEX_DIR_NAME_HIT_SPECIES | String |
index directory name |
|
| PARAM_LOGFILE_NAME_QUERY_SPECIES | String |
logfile name |
|
| PARAM_INDEX_DIR_NAME_QUERY_SPECIES | String |
index directory name |
|
| PARAM_INPUT_FASTA_FILE_HIT_SPECIES | File [FASTA search results format] |
input fasta file |
|
| PARAM_INPUT_FASTA_FILE_QUERY_SPECIES | File [FASTA search results format] |
input fasta file |
|
| PARAM_RETRIEVE_RESULT_FILE_NAME_HIT_SPECIES | String |
retrieve result file name |
|
| PARAM_OUTPUT_SEQRETSPLIT_DIR_NAME_HIT_SPECIES | String |
output directory name |
|
| PARAM_RETRIEVE_RESULT_FILE_NAME_QUERY_SPECIES | String |
retrieve result file name |
|
| PARAM_OUTPUT_SEQRETSPLIT_DIR_NAME_QUERY_SPECIES | String |
output directory name |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| blastdbcmd_hit_species |
../Tools/15_blastdbcmd.cwl
(CommandLineTool)
|
||
| makeblastdb_hit_species |
../Tools/14_makeblastdb.cwl
(CommandLineTool)
|
makeblastdb command for blastdbcmd execution | |
| seqretsplit_hit_species |
../Tools/16_seqretsplit.cwl
(CommandLineTool)
|
||
| blastdbcmd_query_species |
../Tools/15_blastdbcmd.cwl
(CommandLineTool)
|
||
| makeblastdb_query_species |
../Tools/14_makeblastdb.cwl
(CommandLineTool)
|
makeblastdb command for blastdbcmd execution | |
| seqretsplit_query_species |
../Tools/16_seqretsplit.cwl
(CommandLineTool)
|
||
| local_alignment_using_water |
../Tools/17_water.cwl
(CommandLineTool)
|
||
| global_alignment_using_needle |
../Tools/17_needle.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_dir_hit_species | Directory | ||
| output_water_result_dir | Directory | ||
| output_dir_query_species | Directory | ||
| output_needle_result_dir | Directory | ||
| output_water_result_file | File[] | ||
| output_needle_result_file | File[] | ||
| output_logfile_hit_species | File | ||
| output_index_dir_hit_species | Directory | ||
| output_logfile_query_species | File | ||
| output_index_file_hit_species | File | ||
| output_index_dir_query_species | Directory | ||
| output_index_file_query_species | File | ||
| output_blastdbcmd_result_hit_species | File | ||
| output_split_fasta_files_hit_species | File[] | ||
| output_blastdbcmd_result_query_species | File | ||
| output_split_fasta_files_query_species | File[] |
Permalink:
https://w3id.org/cwl/view/git/9bd80581d7ced3ee307b020eb4b091e411c3cbfb/Workflow/11_retrieve_sequence_wf.cwl
