Command Line Interface

This page is meant as a guide for running your own data using either AWS or an HPC. Follow setup commands on the respective pages.

Two Command Line Options Exist for runing this pipeline:

Json File Input
Verbose Command

Example Commands

python3 CLI_hpc.py --json sample.json
python3 CLI.py --json sample.json
sbatch IMD_hpc_in_background.sh
python3 CLI.py --ExpName Test_One --ExpType Stepped --ToolType PW MZ AC --PP ../test-data/SteppedField/II_Preprocessed --IMSMeta ../test-data/SteppedField/IV_ImsMetadata --ACConfig ../test-data/SteppedField/autoCCS_config.xml --TLF ../test-data/SteppedField/TargetList_NeutralMass.csv --mzML /absolute/path/to/III_mzML --FF /absolute/path/to/IV_Features --AutoCCS /absolute/path/to/IV_data

Note: Running the verbose command option will generate a json file called sample.json. This will overwrite any existing sample.json file in the directory.

JSON Input Requirements

ExpName: Experiment Name - Any name you desire. Avoid spacemarks and special characters besides underscores and dashes.
ExpType: Experiment Type - Options are Single, Stepped, or SLIM
ToolType: Tools you’d like to run. Options are PW, MZ, or AC. It is highly reccomended to run these sequentially or in a single pipeline.
Data Folders - Options depend on the tool(s) you’d like to run. More information is below.

Some potential bugs currently exist with file pathing. Note to dev - fix this.

The use of absolute paths is required for any docker mounts, this consists of the three files in the example that use absolue paths. Either relative or absolute paths can be used to specify data locations.

Example JSON File

[
    {
        "ExpName": "Test_One",
        "ExpType": "Stepped",
        "ToolType": [
            "PW",
            "MZ",
            "AC"
        ]
    },
    {
        "PreProcessed Data Folder": "../test-data/SteppedField/II_Preprocessed",
        "IMS Metadata Folder": "../test-data/SteppedField/IV_ImsMetadata",
        "AutoCCS Config File": "../test-data/SteppedField/autoCCS_config.xml",
        "Target List File": "../test-data/SteppedField/TargetList_NeutralMass.csv",
        "mzML Data Folder": "/people/UserName/ion-mob-ms/HPC/III_mzML",
        "Feature Data Folder": "/people/UserName/ion-mob-ms/HPC/IV_Features_csv",
        "AutoCCS Results": "/people/UserName/ion-mob-ms/HPC/IV_data"
    }
]

Verbose Command Line Options

General Commands
Command Description	Path to Json	Experiment Name	Experiment Type	Tool Type, multiple arguments accepted.
Command	`--json`	`--ExpName`	`--ExpType`	`--ToolType`
Command Shorthand	`-j`	`-n`	`-e`	`-t`

Required Commands And Files For Each **Pipeline**
Experiment	Command	Command Shorthand	SingleField	SteppedField	SLIM
PreProcessed Data Folder	`--PP`	`-p`	Yes	Yes	Yes
mzML Data Folder	`--mzML`	`-m`	Yes	Yes	Yes
Feature Data Folder	`--FF`	`-f`	Yes	Yes	Yes
AutoCCS Results	`--AutoCCS`	`-o`	Yes	Yes	Yes
AutoCCS Config File	`--ACConfig`	`-a`	Yes	Yes	Yes
Target List File	`--TLF`	`-s`	Optional	Yes	Optional
IMS Metadata Folder	`--IMSMeta`	`-i`	Recommended	Yes	No
Calibrant File	`--Calibrant`	`-c`	Yes	No	Yes
Metadata File	`--MetadataFile`	`-z`	No	No	Yes