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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,137 +1,137 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/dna_bimodality", | ||
| "name": "biobb_dna HelParBimodality", | ||
| "title": "Determine binormality/bimodality from a helical parameter series dataset.", | ||
| "description": "Determine binormality/bimodality from a helical parameter series dataset.", | ||
| "type": "object", | ||
| "info": { | ||
| "wrapped_software": { | ||
| "name": "In house", | ||
| "license": "Apache-2.0" | ||
| }, | ||
| "ontology": { | ||
| "name": "EDAM", | ||
| "schema": "http://edamontology.org/EDAM.owl" | ||
| } | ||
| }, | ||
| "required": [ | ||
| "input_csv_file", | ||
| "output_csv_path", | ||
| "output_jpg_path" | ||
| ], | ||
| "properties": { | ||
| "input_csv_file": { | ||
| "type": "string", | ||
| "description": "Path to .csv file with helical parameter series. If `input_zip_file` is passed, this should be just the filename of the .csv file inside .zip", | ||
| "filetype": "input", | ||
| "sample": "https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/series_shift_AT.csv", | ||
| "enum": [ | ||
| ".*\\.csv$" | ||
| ], | ||
| "file_formats": [ | ||
| { | ||
| "extension": ".*\\.csv$", | ||
| "description": "Path to .csv file with helical parameter series. If `input_zip_file` is passed, this should be just the filename of the .csv file inside .zip", | ||
| "edam": "format_3752" | ||
| } | ||
| ] | ||
| }, | ||
| "input_zip_file": { | ||
| "type": "string", | ||
| "description": ".zip file containing the `input_csv_file` .csv file", | ||
| "filetype": "input", | ||
| "sample": null, | ||
| "enum": [ | ||
| ".*\\.zip$" | ||
| ], | ||
| "file_formats": [ | ||
| { | ||
| "extension": ".*\\.zip$", | ||
| "description": "zip file containing the `input_csv_file` .csv file", | ||
| "edam": "format_3987" | ||
| } | ||
| ] | ||
| }, | ||
| "output_csv_path": { | ||
| "type": "string", | ||
| "description": "Path to .csv file where output is saved", | ||
| "filetype": "output", | ||
| "sample": "https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/AT_shift_bimod.csv", | ||
| "enum": [ | ||
| ".*\\.csv$" | ||
| ], | ||
| "file_formats": [ | ||
| { | ||
| "extension": ".*\\.csv$", | ||
| "description": "Path to .csv file where output is saved", | ||
| "edam": "format_3752" | ||
| } | ||
| ] | ||
| }, | ||
| "output_jpg_path": { | ||
| "type": "string", | ||
| "description": "Path to .jpg file where output is saved", | ||
| "filetype": "output", | ||
| "sample": "https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/AT_shift_bimod.jpg", | ||
| "enum": [ | ||
| ".*\\.jpg$" | ||
| ], | ||
| "file_formats": [ | ||
| { | ||
| "extension": ".*\\.jpg$", | ||
| "description": "Path to .jpg file where output is saved", | ||
| "edam": "format_3579" | ||
| } | ||
| ] | ||
| }, | ||
| "properties": { | ||
| "type": "object", | ||
| "properties": { | ||
| "helpar_name": { | ||
| "type": "string", | ||
| "default": "Optional", | ||
| "wf_prop": false, | ||
| "description": "helical parameter name." | ||
| }, | ||
| "confidence_level": { | ||
| "type": "number", | ||
| "default": 5.0, | ||
| "wf_prop": false, | ||
| "description": "Confidence level for Byes Factor test (in percentage)." | ||
| }, | ||
| "max_iter": { | ||
| "type": "integer", | ||
| "default": 400, | ||
| "wf_prop": false, | ||
| "description": "Number of maximum iterations for EM algorithm." | ||
| }, | ||
| "tol": { | ||
| "type": "number", | ||
| "default": 1e-05, | ||
| "wf_prop": false, | ||
| "description": "Tolerance value for EM algorithm." | ||
| }, | ||
| "remove_tmp": { | ||
| "type": "boolean", | ||
| "default": true, | ||
| "wf_prop": true, | ||
| "description": "Remove temporal files." | ||
| }, | ||
| "restart": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "wf_prop": true, | ||
| "description": "Do not execute if output files exist.1" | ||
| }, | ||
| "sandbox_path": { | ||
| "type": "string", | ||
| "default": "./", | ||
| "wf_prop": true, | ||
| "description": "Parent path to the sandbox directory." | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "additionalProperties": false | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/dna_bimodality", | ||
| "name": "biobb_dna HelParBimodality", | ||
| "title": "Determine binormality/bimodality from a helical parameter series dataset.", | ||
| "description": "Determine binormality/bimodality from a helical parameter series dataset.", | ||
| "type": "object", | ||
| "info": { | ||
| "wrapped_software": { | ||
| "name": "In house", | ||
| "license": "Apache-2.0" | ||
| }, | ||
| "ontology": { | ||
| "name": "EDAM", | ||
| "schema": "http://edamontology.org/EDAM.owl" | ||
| } | ||
| }, | ||
| "required": [ | ||
| "input_csv_file", | ||
| "output_csv_path", | ||
| "output_jpg_path" | ||
| ], | ||
| "properties": { | ||
| "input_csv_file": { | ||
| "type": "string", | ||
| "description": "Path to .csv file with helical parameter series. If `input_zip_file` is passed, this should be just the filename of the .csv file inside .zip", | ||
| "filetype": "input", | ||
| "sample": "https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/series_shift_AT.csv", | ||
| "enum": [ | ||
| ".*\\.csv$" | ||
| ], | ||
| "file_formats": [ | ||
| { | ||
| "extension": ".*\\.csv$", | ||
| "description": "Path to .csv file with helical parameter series. If `input_zip_file` is passed, this should be just the filename of the .csv file inside .zip", | ||
| "edam": "format_3752" | ||
| } | ||
| ] | ||
| }, | ||
| "input_zip_file": { | ||
| "type": "string", | ||
| "description": ".zip file containing the `input_csv_file` .csv file", | ||
| "filetype": "input", | ||
| "sample": null, | ||
| "enum": [ | ||
| ".*\\.zip$" | ||
| ], | ||
| "file_formats": [ | ||
| { | ||
| "extension": ".*\\.zip$", | ||
| "description": "zip file containing the `input_csv_file` .csv file", | ||
| "edam": "format_3987" | ||
| } | ||
| ] | ||
| }, | ||
| "output_csv_path": { | ||
| "type": "string", | ||
| "description": "Path to .csv file where output is saved", | ||
| "filetype": "output", | ||
| "sample": "https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/AT_shift_bimod.csv", | ||
| "enum": [ | ||
| ".*\\.csv$" | ||
| ], | ||
| "file_formats": [ | ||
| { | ||
| "extension": ".*\\.csv$", | ||
| "description": "Path to .csv file where output is saved", | ||
| "edam": "format_3752" | ||
| } | ||
| ] | ||
| }, | ||
| "output_jpg_path": { | ||
| "type": "string", | ||
| "description": "Path to .jpg file where output is saved", | ||
| "filetype": "output", | ||
| "sample": "https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/AT_shift_bimod.jpg", | ||
| "enum": [ | ||
| ".*\\.jpg$" | ||
| ], | ||
| "file_formats": [ | ||
| { | ||
| "extension": ".*\\.jpg$", | ||
| "description": "Path to .jpg file where output is saved", | ||
| "edam": "format_3579" | ||
| } | ||
| ] | ||
| }, | ||
| "properties": { | ||
| "type": "object", | ||
| "properties": { | ||
| "helpar_name": { | ||
| "type": "string", | ||
| "default": "Optional", | ||
| "wf_prop": false, | ||
| "description": "helical parameter name." | ||
| }, | ||
| "confidence_level": { | ||
| "type": "number", | ||
| "default": 5.0, | ||
| "wf_prop": false, | ||
| "description": "Confidence level for Byes Factor test (in percentage)." | ||
| }, | ||
| "max_iter": { | ||
| "type": "integer", | ||
| "default": 400, | ||
| "wf_prop": false, | ||
| "description": "Number of maximum iterations for EM algorithm." | ||
| }, | ||
| "tol": { | ||
| "type": "number", | ||
| "default": 1e-05, | ||
| "wf_prop": false, | ||
| "description": "Tolerance value for EM algorithm." | ||
| }, | ||
| "remove_tmp": { | ||
| "type": "boolean", | ||
| "default": true, | ||
| "wf_prop": true, | ||
| "description": "Remove temporal files." | ||
| }, | ||
| "restart": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "wf_prop": true, | ||
| "description": "Do not execute if output files exist." | ||
| }, | ||
| "sandbox_path": { | ||
| "type": "string", | ||
| "default": "./", | ||
| "wf_prop": true, | ||
| "description": "Parent path to the sandbox directory.1" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "additionalProperties": false | ||
| } |
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