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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