From 0ddaa25b6a66596c2bcb77a47762794d1b836b44 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Thu, 4 Jul 2024 10:48:03 +0200 Subject: [PATCH] [UPDATE] Adding sandbox_path property to the json schemas --- biobb_dna/docs/source/command_line.md | 46 +--- biobb_dna/json_schemas/dna_bimodality.json | 270 ++++++++++----------- 2 files changed, 143 insertions(+), 173 deletions(-) diff --git a/biobb_dna/docs/source/command_line.md b/biobb_dna/docs/source/command_line.md index 4ed48505..f5bce03b 100644 --- a/biobb_dna/docs/source/command_line.md +++ b/biobb_dna/docs/source/command_line.md @@ -397,21 +397,7 @@ Command: ```python canal_unzip -h ``` - usage: canal_unzip [-h] [--config CONFIG] --input_zip_file INPUT_ZIP_FILE --output_path OUTPUT_PATH [--output_list_path OUTPUT_LIST_PATH] - - Tool for extracting biobb_canal output files. - - optional arguments: - -h, --help show this help message and exit - --config CONFIG Configuration file - --output_list_path OUTPUT_LIST_PATH - Text file with a list of all Canal output files contained within input_zip_file. Accepted formats: txt. - - required arguments: - --input_zip_file INPUT_ZIP_FILE - Zip file with Canal output files. Accepted formats: zip. - --output_path OUTPUT_PATH - Canal output file contained within input_zip_file. Accepted formats: ser, his, cor. + /bin/sh: canal_unzip: command not found ### I / O Arguments Syntax: input_argument (datatype) : Definition @@ -691,15 +677,15 @@ Command: dna_bimodality -h ``` usage: dna_bimodality [-h] [--config CONFIG] --input_csv_file INPUT_CSV_FILE [--input_zip_file INPUT_ZIP_FILE] --output_csv_path OUTPUT_CSV_PATH --output_jpg_path OUTPUT_JPG_PATH - + Determine binormality/bimodality from a helical parameter dataset. - - options: + + optional arguments: -h, --help show this help message and exit --config CONFIG Configuration file --input_zip_file INPUT_ZIP_FILE Path to zip file containing csv input files. Accepted formats: zip. - + required arguments: --input_csv_file INPUT_CSV_FILE Path to csv file with data. Accepted formats: csv. @@ -724,8 +710,8 @@ Config parameters for this building block: * **max_iter** (*integer*): (400) Number of maximum iterations for EM algorithm.. * **tol** (*number*): (1e-05) Tolerance value for EM algorithm.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. -* **restart** (*boolean*): (False) Do not execute if output files exist.1. -* **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. +* **restart** (*boolean*): (False) Do not execute if output files exist.. +* **sandbox_path** (*string*): (./) Parent path to the sandbox directory.1. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_dna/blob/master/biobb_dna/test/data/config/config_dna_bimodality.yml) ```python @@ -979,23 +965,7 @@ Command: ```python dna_timeseries_unzip -h ``` - usage: dna_timeseries_unzip [-h] [--config CONFIG] --input_zip_file INPUT_ZIP_FILE --output_path_csv OUTPUT_PATH_CSV --output_path_jpg OUTPUT_PATH_JPG [--output_list_path OUTPUT_LIST_PATH] - - Tool for extracting dna_timeseries output files. - - optional arguments: - -h, --help show this help message and exit - --config CONFIG Configuration file - --output_list_path OUTPUT_LIST_PATH - Text file with a list of all dna_timeseries output files contained within input_zip_file. Accepted formats: txt. - - required arguments: - --input_zip_file INPUT_ZIP_FILE - Zip file with dna_timeseries output files. Accepted formats: zip. - --output_path_csv OUTPUT_PATH_CSV - dna_timeseries output csv file contained within input_zip_file. Accepted formats: csv. - --output_path_jpg OUTPUT_PATH_JPG - dna_timeseries output jpg file contained within input_zip_file. Accepted formats: jpg. + /bin/sh: dna_timeseries_unzip: command not found ### I / O Arguments Syntax: input_argument (datatype) : Definition diff --git a/biobb_dna/json_schemas/dna_bimodality.json b/biobb_dna/json_schemas/dna_bimodality.json index 012b12f0..492a55c4 100644 --- a/biobb_dna/json_schemas/dna_bimodality.json +++ b/biobb_dna/json_schemas/dna_bimodality.json @@ -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 } \ No newline at end of file