CWL Workflow: Averages and aligns the unampped instances

Workflow: Averages and aligns the unampped instances

Fetched 2024-11-26 00:25:45 GMT

Verified with cwltool version 3.1.20230201224320

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.

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This workflow is Open Source and may be reused according to the terms of: https://gitlab.inria.fr/capsid.public_codes/CroMaSt.git

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title
pdb_dir	Directory	The directory with (or to store) PDB files
iteration	Integer	Iteration number
core_struct	File [PDB]	Core average structure
failed_name	String	To store StIs failed to pass the threshold
passed_name	String	To store StIs passing the threshold
unmapped_list	File [JSON]	List of un-mapped domin StIs
alignment_score	String	Alignment score from Kpax to analyse structures
score_threshold	Float	Score threshold for given alignment score from Kpax

Steps

ID	Runs	Label	Doc
copy_avg_dom	move_files.cwl (CommandLineTool)	Moves passed files to given directory	The tool copy all the files from their original location to the directory provided by user.
avg_unp_domains	bd3377bfc57b3d007de7b0995d2023bb (Workflow)
check_threshold_step	filter_align_scores.cwl (CommandLineTool)	Filter all structural instances for given Pfam families.	The tool filter raw files from Pfam to retrieves all the available structural instances from the given Pfam families. cwl-runner --cachedir=tmp_files/ --outdir=Results/ Workflow/separate_structures.cwl yml/separate_structures.yml
per_unp_dom_instance	crossmapped_per_unp_dom.cwl (CommandLineTool)	Divides a dictionary of structures per family into multiple according to domain instance	The tool takes a dictionary and divides all the structures according to their UniProt id and domain position.
pairwise_align_avg_structs	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

Outputs

ID	Type	Label
domain_like_list	File [CSV]	Domain-like StIs
failed_domains_list	File [CSV]	Failed domain StIs
unmapped_aligned_results	File [CSV]	Alignment results from Kpax for unmapped instances

Permalink: https://w3id.org/cwl/view/git/b5a9d4b025ec8e065bae97eeb96f10db2dd8e1e6/Tools/unmapped_unp_avg_align.cwl