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[UPDATE] Adding sandbox_path property to the json schemas
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@PauAndrio
PauAndrio committed Jul 4, 2024
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46 changes: 8 additions & 38 deletions biobb_dna/docs/source/command_line.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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.
Expand All @@ -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
Expand Down Expand Up @@ -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

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270 changes: 135 additions & 135 deletions biobb_dna/json_schemas/dna_bimodality.json
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@@ -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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