CLI Options
There are many customizable parameters for the xlranker CLI. To view all of the options, you can run
Usage: xlranker start [ARGS] [OPTIONS]
Run the full prioritization pipeline
Requires input file to be in the format specified in the project documentation.
╭─ Parameters ────────────────────────────────────────────────────────────────────╮
│ NETWORK --network -n path to TSV file containing peptide │
│ network. │
│ DATA-FOLDER --data-folder -d folder containing the omics data for the │
│ model prediction. │
│ CONFIG --config -c if set, read and load options from config │
│ file. Can be in JSON or YAML format. │
│ SEED --seed -s seed for machine learning pipeline. If not │
│ set, seed is randomly selected. │
│ VERBOSE --verbose --no-verbose -v enable verbose logging. [default: False] │
│ LOG-FILE --log-file -l if set, saves logging to path │
│ MAPPING-TABLE --mapping-table -m path to custom mapping table for peptide │
│ sequences │
│ SPLIT --split character used for splitting the FASTA file │
│ header │
│ GS-INDEX --gs-index index in the FASTA file that contains the │
│ gene symbol. Index starts at 0. │
│ IS-FASTA --is-fasta Enable if mapping table is a FASTA file. │
│ --no-is-fasta [default: False] │
╰─────────────────────────────────────────────────────────────────────────────────╯
Instead of setting these parameters each run, you can create a config file. To create the config file, run xlranker init or view the documentation.