# BioBB TEMPLATE Command Line Help Generic usage: ```python biobb_command [-h] --config CONFIG --input_file(s) --output_file ``` ----------------- ## Template Short description for the template module in Restructured Text (reST) syntax. Mandatory. ### Get help Command: ```python template -h ``` usage: template [-h] [-c CONFIG] --input_file_path1 INPUT_FILE_PATH1 [--input_file_path2 INPUT_FILE_PATH2] -o OUTPUT_FILE_PATH Description for the template module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string --input_file_path2 INPUT_FILE_PATH2 Description for the second input file path (optional). Accepted formats: dcd. required arguments: --input_file_path1 INPUT_FILE_PATH1 Description for the first input file path. Accepted formats: top. -o OUTPUT_FILE_PATH, --output_file_path OUTPUT_FILE_PATH Description for the output file path. Accepted formats: zip. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_file_path1** (*string*): Description for the first input file path. File type: input. [Sample file](https://urlto.sample). Accepted formats: TOP * **input_file_path2** (*string*): Description for the second input file path (optional). File type: input. [Sample file](https://urlto.sample). Accepted formats: DCD * **output_file_path** (*string*): Description for the output file path. File type: output. [Sample file](https://urlto.sample). Accepted formats: ZIP ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **boolean_property** (*boolean*): (True) Example of boolean property.. * **binary_path** (*string*): (zip) Example of executable binary property.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_template/blob/master/biobb_template/test/data/config/config_template.yml) ```python properties: boolean_property: false remove_tmp: true ``` #### [Docker config file](https://github.com/bioexcel/biobb_template/blob/master/biobb_template/test/data/config/config_template_docker.yml) ```python properties: boolean_property: false container_image: mmbirb/zip:latest container_path: docker container_volume_path: /tmp remove_tmp: true ``` #### [Singularity config file](https://github.com/bioexcel/biobb_template/blob/master/biobb_template/test/data/config/config_template_singularity.yml) ```python properties: binary_path: /opt/conda/bin/zip boolean_property: false container_image: bioexcel-zip_container-master-latest.simg container_path: singularity container_volume_path: /tmp remove_tmp: false ``` #### Command line ```python template --config config_template.yml --input_file_path1 urlto.sample --input_file_path2 urlto.sample --output_file_path urlto.sample ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_template/blob/master/biobb_template/test/data/config/config_template.json) ```python { "properties": { "boolean_property": false, "remove_tmp": true } } ``` #### [Docker config file](https://github.com/bioexcel/biobb_template/blob/master/biobb_template/test/data/config/config_template_docker.json) ```python { "properties": { "boolean_property": false, "remove_tmp": true, "container_path": "docker", "container_image": "mmbirb/zip:latest", "container_volume_path": "/tmp" } } ``` #### [Singularity config file](https://github.com/bioexcel/biobb_template/blob/master/biobb_template/test/data/config/config_template_singularity.json) ```python { "properties": { "boolean_property": false, "remove_tmp": false, "binary_path": "/opt/conda/bin/zip", "container_path": "singularity", "container_image": "bioexcel-zip_container-master-latest.simg", "container_volume_path": "/tmp" } } ``` #### Command line ```python template --config config_template.json --input_file_path1 urlto.sample --input_file_path2 urlto.sample --output_file_path urlto.sample ``` ## Template_container Short description for the template container module in Restructured Text (reST) syntax. Mandatory. ### Get help Command: ```python template_container -h ``` /bin/sh: 1: template_container: not found ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_file_path1** (*string*): Description for the first input file path. File type: input. [Sample file](https://urlto.sample). Accepted formats: TOP * **input_file_path2** (*string*): Description for the second input file path (optional). File type: input. [Sample file](https://urlto.sample). Accepted formats: DCD * **output_file_path** (*string*): Description for the output file path. File type: output. [Sample file](https://urlto.sample). Accepted formats: ZIP ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **boolean_property** (*boolean*): (True) Example of boolean property.. * **binary_path** (*string*): (zip) Example of executable binary property.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. * **container_path** (*string*): (None) Container path definition.. * **container_image** (*string*): (mmbirb/zip:latest) Container image definition.. * **container_volume_path** (*string*): (/tmp) Container volume path definition.. * **container_working_dir** (*string*): (None) Container working directory definition.. * **container_user_id** (*string*): (None) Container user_id definition.. * **container_shell_path** (*string*): (/bin/bash) Path to default shell inside the container.. ### YAML ### JSON