diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg index 70570e2a..a707a97c 100644 --- a/docs/images/sequence-help.svg +++ b/docs/images/sequence-help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + - + - + - - $ casanovo sequence --help - -Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 - - De novo sequence peptides from tandem mass spectra.                             - PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence  - peptides. If evaluate is set to True PEAK_PATH must be one or more annotated    - MGF file.                                                                       - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*  PEAK_PATH    FILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--evaluate-e  Run in evaluation mode. When    │ -│                                              this flag is set the peptide    │ -│                                              and amino acid precision will   │ -│                                              be calculated and logged at the │ -│                                              end of the sequencing run. All  │ -│                                              input files must be annotated   │ -│                                              MGF files if running in         │ -│                                              evaluation mode.                │ -│--model-mTEXT                        Either the model weights (.ckpt │ -│                                              file) or a URL pointing to the  │ -│                                              model weights file. If not      │ -│                                              provided, Casanovo will try to  │ -│                                              download the latest release     │ -│                                              automatically.                  │ -│--output-oFILE                        The mzTab file to which results │ -│                                              will be written.                │ -│--config-cFILE                        The YAML configuration file     │ -│                                              overriding the default options. │ -│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ -│                                              logging messages. Log files are │ -│                                              always set to 'debug'.          │ -│--help-h  Show this message and exit.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo sequence --help + +Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 + + De novo sequence peptides from tandem mass spectra.                             + PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence  + peptides. If evaluate is set to True PEAK_PATH must be one or more annotated    + MGF file.                                                                       + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--evaluate-e  Run in evaluation mode. When  │ +│                                                this flag is set the peptide  │ +│                                                and amino acid precision will │ +│                                                be calculated and logged at   │ +│                                                the end of the sequencing     │ +│                                                run. All input files must be  │ +│                                                annotated MGF files if        │ +│                                                running in evaluation mode.   │ +│--model-mTEXT                        Either the model weights      │ +│                                                (.ckpt file) or a URL         │ +│                                                pointing to the model weights │ +│                                                file. If not provided,        │ +│                                                Casanovo will try to download │ +│                                                the latest release            │ +│                                                automatically.                │ +│--output_dir-fPATH                        The destination directory for │ +│                                                output files                  │ +│--output_root-oFILE                        The root name for all output  │ +│                                                files                         │ +│--config-cFILE                        The YAML configuration file   │ +│                                                overriding the default        │ +│                                                options.                      │ +│--verbosity-v[debug|info|warning|error]  Set the verbosity of console  │ +│                                                logging messages. Log files   │ +│                                                are always set to 'debug'.    │ +│--overwrite-d  Whether to overwrite output   │ +│                                                files.                        │ +│--help-h  Show this message and exit.   │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/train-help.svg b/docs/images/train-help.svg index e27717e1..f5fd20a7 100644 --- a/docs/images/train-help.svg +++ b/docs/images/train-help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + - + - + - - $ casanovo train --help - -Usage:casanovo train [OPTIONS] TRAIN_PEAK_PATH...                              - - Train a Casanovo model on your own data.                                        - TRAIN_PEAK_PATH must be one or more annoated MGF files, such as those provided  - by MassIVE-KB, from which to train a new Casnovo model.                         - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*  TRAIN_PEAK_PATH    FILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│*--validation_peak_pa…-pFILE                    An annotated MGF file  │ -│                                                       for validation, like   │ -│                                                       from MassIVE-KB. Use   │ -│                                                       this option multiple   │ -│                                                       times to specify       │ -│                                                       multiple files.        │ -│[required]            │ -│--model-mTEXT                    Either the model       │ -│                                                       weights (.ckpt file)   │ -│                                                       or a URL pointing to   │ -│                                                       the model weights      │ -│                                                       file. If not provided, │ -│                                                       Casanovo will try to   │ -│                                                       download the latest    │ -│                                                       release automatically. │ -│--output-oFILE                    The mzTab file to      │ -│                                                       which results will be  │ -│                                                       written.               │ -│--config-cFILE                    The YAML configuration │ -│                                                       file overriding the    │ -│                                                       default options.       │ -│--verbosity-v[debug|info|warning|er  Set the verbosity of   │ -│ror]  console logging        │ -│                                                       messages. Log files    │ -│                                                       are always set to      │ -│                                                       'debug'.               │ -│--help-h  Show this message and  │ -│                                                       exit.                  │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo train --help + +Usage:casanovo train [OPTIONS] TRAIN_PEAK_PATH...                              + + Train a Casanovo model on your own data.                                        + TRAIN_PEAK_PATH must be one or more annoated MGF files, such as those provided  + by MassIVE-KB, from which to train a new Casnovo model.                         + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  TRAIN_PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--validation_peak_path-pFILE                    An annotated MGF file    │ +│                                                     for validation, like     │ +│                                                     from MassIVE-KB. Use     │ +│                                                     this option multiple     │ +│                                                     times to specify         │ +│                                                     multiple files.          │ +│--model-mTEXT                    Either the model weights │ +│                                                     (.ckpt file) or a URL    │ +│                                                     pointing to the model    │ +│                                                     weights file. If not     │ +│                                                     provided, Casanovo will  │ +│                                                     try to download the      │ +│                                                     latest release           │ +│                                                     automatically.           │ +│--output_dir-fPATH                    The destination          │ +│                                                     directory for output     │ +│                                                     files                    │ +│--output_root-oFILE                    The root name for all    │ +│                                                     output files             │ +│--config-cFILE                    The YAML configuration   │ +│                                                     file overriding the      │ +│                                                     default options.         │ +│--verbosity-v[debug|info|warning|er  Set the verbosity of     │ +│ror]  console logging          │ +│                                                     messages. Log files are  │ +│                                                     always set to 'debug'.   │ +│--overwrite-d  Whether to overwrite     │ +│                                                     output files.            │ +│--help-h  Show this message and    │ +│                                                     exit.                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +