Workflow: CroMaSt.cwl
Fetched 2024-11-25 09:40:52 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| cath | String[] (Optional) | CATH family ids | |
| pfam | String[] (Optional) | Pfam family ids | |
| pdbDir | Directory | The directory for storing all PDB files | |
| filename | File | Filename to store family ids per iteration | |
| siftsDir | Directory | Directory for storing all SIFTS files | |
| cath_lost | String | Obsolete and inconsistent CATH domain StIs | |
| iteration | Integer | Iteration number starting from 0 | |
| paramfile | File [YAML] | Parameter file for current iteration | |
| pfam_lost | String | Obsolete and inconsistent Pfam domain StIs | |
| cath_resmap | String | Filename for residue-mapped CATH domain StIs | |
| db_for_core | String | Database to select to compute core average structure | |
| domain_like | File | To store all the domain-like StIs | |
| pfam_resmap | String | Filename for residue-mapped Pfam domain StIs | |
| failed_domain | File | To store all failed domain StIs | |
| alignment_score | String | Alignment score from Kpax to analyse structures | |
| score_threshold | Float | Score threshold for given alignment score from Kpax | |
| unmap_cath_fail | String | Filename to store unmapped and not properly aligned instances from CATH | |
| unmap_cath_pass | String | Filename to store unmapped but structurally well aligned instances from CATH | |
| unmap_pfam_fail | String | Filename to store unmapped and not properly aligned instances from Pfam | |
| unmap_pfam_pass | String | Filename to store unmapped but structurally well aligned instances from Pfam | |
| true_domain_file | File | To store all the true domain StIs | |
| min_domain_length | Integer | Threshold for minimum domain length | |
| core_domain_struct | File | Core domain structure (.pdb) | |
| prev_crossMapped_cath | File | CATH cross-mapped domain StIs from previous iteration | |
| prev_crossMapped_pfam | File | Pfam cross-mapped domain StIs from previous iteration | |
| unmapped_analysis_file | String | Filename with alignment scores for unmapped instances |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| get_family_ids |
Tools/get_family_ids.cwl
(CommandLineTool)
|
Get domain family ids |
Get domain family ids from CATH and Pfam databases from parameter file provided by user and write these ids to a separate file. |
| format_core_list |
Tools/list_true_domains.cwl
(CommandLineTool)
|
Format core domain instance list |
Fornat core domain instances list from the common instances list identified at first iteration; Preparing input for average structure computation |
| gather_domain_like |
Tools/merge_df2json.cwl
(CommandLineTool)
|
Merge all passed domain instances together |
Helps to collect all domain instances passed to this tool and outputs the list with all these domain instances together. |
| unmapped_from_cath |
Tools/unmapped_unp_avg_align.cwl
(Workflow)
|
Averages and aligns the unampped instances |
First computes average per UniProt domain instance and then aligns all the average structures against core average structure. Outputs the alignment results along with the structures passing and failing the threshold for given Kpax score. |
| unmapped_from_pfam |
Tools/unmapped_unp_avg_align.cwl
(Workflow)
|
Averages and aligns the unampped instances |
First computes average per UniProt domain instance and then aligns all the average structures against core average structure. Outputs the alignment results along with the structures passing and failing the threshold for given Kpax score. |
| cath_domain_instances |
Tools/resmapping_cath_instances_subwf.cwl
(Workflow)
|
Produce a list of residue-mapped structural domain instances from CATH ids |
Retrieve and process the PDB structures corresponding to the CATH superfamily ids resulting in a list of residue-mapped structural domain instances along with lost structural instances (requires Data/cath_domain_description_file.txt downloaded from CATH and uses SIFTS resource for PDB to UniProt residue Mapping) |
| chop_and_avg_for_core |
Tools/core_avg_subwf.cwl
(Workflow)
|
Compute average of average for core domain instances |
Compute average structure for all averaged structures corresponding to core UniProt domain instances. First computes average per UniProt domain instance and then average all averaged structures. |
| create_new_parameters |
Tools/create_param.cwl
(CommandLineTool)
|
Create parameter file for next iteration |
Create parameter file for next iteration from previous parameter file Filter the pairwise alignments to retrieve family ids passing the threshold for a given Kpax score type |
| gather_failed_domains |
Tools/merge_df2json.cwl
(CommandLineTool)
|
Merge all passed domain instances together |
Helps to collect all domain instances passed to this tool and outputs the list with all these domain instances together. |
| pfam_domain_instances |
Tools/resmapping_pfam_instances_subwf.cwl
(Workflow)
|
Produce a list of residue-mapped structural domain instances from Pfam ids |
Retrieve and process the PDB structures corresponding to the Pfam family ids resulting in a list of residue-mapped structural domain instances along with lost structural instances (requires Data/pdbmap downloaded from Pfam and uses SIFTS resource for UniProt to PDB residue Mapping) |
| check_alignment_scores |
Tools/check_threshold.cwl
(CommandLineTool)
|
Checks the alignment score for given threshold |
Checks the alignment score for each aligned structure based on the given threshold Outputs the structural instances passing and failing the threshold in separate files |
| crossmapping_CATH2Pfam |
Tools/map_unique_struct_cath2pfam.cwl
(CommandLineTool)
|
Map unique CATH instances to Pfam db |
Maps the unique instances from CATH to the whole Pfam database (using residue numbering from UniProt allowing variable domain boundaries, by default +/-30aa) |
| crossmapping_Pfam2CATH |
Tools/map_unique_struct_pfam2cath.cwl
(CommandLineTool)
|
Map unique Pfam instances to CATH db |
Maps the unique instances from Pfam to the whole CATH database (using residue numbering from PDB allowing variable domain boundaries, by default +/-30aa) |
| align_avg_structs_pairwise |
Tools/pairwise_aligner.cwl
(CommandLineTool)
|
Pairwise structural alignemnt using Kpax |
Align crossmapped averaged structures against core average domain structure pairwise using Kpax Outputs a csv file with all the scores from pairwise alignments |
| chop_and_avg_for_CATH2Pfam |
Tools/other_avg_subwf.cwl
(Workflow)
|
Compute average of average per cross-mapped famil(y)ies |
Compute average structure for all averaged structures corresponding to UniProt domain instances cross-mapped from Pfam/CATH to a CATH/Pfam family. First computes average per UniProt domain instance and then average all averaged structures per Pfam family. |
| chop_and_avg_for_Pfam2CATH |
Tools/other_avg_subwf.cwl
(Workflow)
|
Compute average of average per cross-mapped famil(y)ies |
Compute average structure for all averaged structures corresponding to UniProt domain instances cross-mapped from Pfam/CATH to a CATH/Pfam family. First computes average per UniProt domain instance and then average all averaged structures per Pfam family. |
| compare_instances_CATH_Pfam |
Tools/compare_cath_pfam.cwl
(CommandLineTool)
|
Compare residue-mapped instances from Pfam and CATH |
Find the intersection between residue-mapped instances of Pfam and CATH lists. Allows variable domain boundaries in a certain range +/- 30aa. Produces three files: common domain instances, and unique domain instances to each Pfam and CATH. |
| add_crossmapped_to_resmapped |
Tools/add_crossmapped2resmapped.cwl
(CommandLineTool)
|
Add cross-mapped structural instances to residue-mapped structural instances |
Add crossmapped domain instances from last iteration to current list of residue mapped domain instances. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| unmap_cath | File [JSON] | All un-mapped domin StIs from CATH | |
| unmap_pfam | File [JSON] | All Pfam un-mapped domin StIs | |
| allmap_cath | File [JSON] | All CATH cross-mapped domin StIs family-wise together | |
| allmap_pfam | File [JSON] | All Pfam domain StIs cross-mapped to CATH family-wise | |
| family_ids_x | File [JSON] | Family ids per iteration | |
| reslost_cath | File [JSON] | Obsolete and inconsistent domain StIs from CATH | |
| reslost_pfam | File [JSON] | Obsolete and inconsistent domain StIs from Pfam | |
| true_domains | File [JSON] | True domain StIs per iteration | |
| crossmap_cath | File[] [JSON] | CATH domain StIs cross-mapped to Pfam family-wise | |
| crossmap_pfam | File[] [JSON] | Pfam domin StIs cross-mapped to CATH family-wise | |
| next_parmfile | File [YAML] | Parameter file for next iteration of the workflow | |
| core_structure | File (Optional) | Core domain structure (.pdb) | |
| resmapped_cath | File [CSV] | All CATH residue-mapped domain StIs with domain labels | |
| resmapped_pfam | File [CSV] | All Pfam residue-mapped domain StIs with domain labels | |
| all_domain_like | File [JSON] | Domain-like StIs | |
| align_unmap_cath | File [CSV] | Alignment results for CATH unmapped instances | |
| align_unmap_pfam | File [CSV] | Alignment results for Pfam unmapped instances | |
| core_domains_list | File (Optional) [JSON] | Core domain StIs | |
| unmap_cath_failed | File [CSV] | Failed domain StIs from CATH | |
| unmap_cath_passed | File [CSV] | Domain-like StIs from CATH | |
| unmap_pfam_failed | File [CSV] | Failed domain StIs from Pfam | |
| unmap_pfam_passed | File [CSV] | Domain-like StIs from Pfam | |
| all_failed_domains | File [JSON] | Failed domain StIs | |
| crossres_mappedcath | File [CSV] | Merged cross-mapped and residue-mapped domain StIs from CATH | |
| crossres_mappedpfam | File [CSV] | Merged cross-mapped and residue-mapped domain StIs from Pfam | |
| avg_alignment_result | File [CSV] | Alignment results from Kpax for all cross-mapped families | |
| cath_crossmap_pfam_avg | File[] [PDB] | Average structures per cross-mapped Pfam family for CATH StIs at family level | |
| pfam_crossmap_cath_avg | File[] [PDB] | Average structures per cross-mapped CATH family for Pfam StIs at family level | |
| crossmapped_cath_passed | File [JSON] | Cross-mapped families with CATH domain StIs passing the threshold | |
| crossmapped_pfam_passed | File [JSON] | Cross-mapped families with Pfam domain StIs passing the threshold |
https://w3id.org/cwl/view/git/b5a9d4b025ec8e065bae97eeb96f10db2dd8e1e6/CroMaSt.cwl
