# BioBB TEMPLATE Command Line Help
Generic usage:
`python
biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>
`
—————–
## Template_container
Short description for the template container module in Restructured Text (reST) syntax. Mandatory.
### Get help
Command:
`python
template_container -h
`
usage: template_container [-h] [–config CONFIG] –input_file_path1 INPUT_FILE_PATH1 [–input_file_path2 INPUT_FILE_PATH2] –output_file_path OUTPUT_FILE_PATH
Description for the template container module.
- optional arguments:
- -h, --help
show this help message and exit
- --config CONFIG
Configuration file
- --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.
- --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.. * executable_binary_property (string): (zip) Example of executable binary property.. * remove_tmp (boolean): (True) Remove temporal files.. * restart (boolean): (False) Do not execute if output files exist.. * 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 #### [Common config file](https://github.com/bioexcel/biobb_template/blob/master/biobb_template/test/data/config/config_template_container.yml) ```python properties:
boolean_property: false container_image: mmbirb/zip:latest container_path: docker container_volume_path: /tmp remove_tmp: true
`
#### Command line
```python
template_container --config config_template_container.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_container.json)
```python
{
- “properties”: {
“boolean_property”: false, “remove_tmp”: true, “container_path”: “docker”, “container_image”: “mmbirb/zip:latest”, “container_volume_path”: “/tmp”
}
}
#### Command line
`python
template_container --config config_template_container.json --input_file_path1 urlto.sample --input_file_path2 urlto.sample --output_file_path urlto.sample
`
## Template
Short description for the template module in Restructured Text (reST) syntax. Mandatory.
### Get help
Command:
`python
template -h
`
usage: template [-h] [–config CONFIG] –input_file_path1 INPUT_FILE_PATH1 [–input_file_path2 INPUT_FILE_PATH2] –output_file_path OUTPUT_FILE_PATH
Description for the template module.
- optional arguments:
- -h, --help
show this help message and exit
- --config CONFIG
Configuration file
- --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.
- --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.. * executable_binary_property (string): (zip) Example of executable binary property.. * remove_tmp (boolean): (True) Remove temporal files.. * restart (boolean): (False) Do not execute if output files exist.. ### 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
``` #### [Singularity config file](https://github.com/bioexcel/biobb_template/blob/master/biobb_template/test/data/config/config_template_singularity.yml) ```python properties:
boolean_property: false container_image: bioexcel-zip_container-master-latest.simg container_path: singularity container_volume_path: /tmp executable_binary_property: /opt/conda/bin/zip 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
}
}
#### [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, “executable_binary_property”: “/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
`