From ada111826a154c6bc5a1472cb533c349afae965b Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 20 Nov 2024 17:58:51 +0000 Subject: [PATCH] Generate new screengrabs with rich-codex --- docs/images/db-search-help.svg | 179 ++++++++++++++++++++++++++------- 1 file changed, 141 insertions(+), 38 deletions(-) diff --git a/docs/images/db-search-help.svg b/docs/images/db-search-help.svg index b1fcce10..6e05dcc5 100644 --- a/docs/images/db-search-help.svg +++ b/docs/images/db-search-help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ casanovo configure --help - -Usage:casanovo configure [OPTIONS]                                             - - Generate a Casanovo configuration file to customize.                            - The casanovo configuration file is in the YAML format.                          - -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--output-oFILE  The output configuration file.                           │ -│--help-h  Show this message and exit.                              │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo db-search --help + +Usage:casanovo db-search [OPTIONS] PEAK_PATH... FASTA_PATH + + Perform a database search on MS/MS data using Casanovo-DB.                      + PEAK_PATH must be one or more mzML, mzXML, or MGF files. FASTA_PATH must be     + one FASTA file.                                                                 + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  PEAK_PATH     FILE[required]│ +│*  FASTA_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--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-dPATH                       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'.                │ +│--force_overwrite-f  Whether to overwrite       │ +│                                                   output files.              │ +│--help-h  Show this message and      │ +│                                                   exit.                      │ +╰──────────────────────────────────────────────────────────────────────────────╯ +