diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg
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@@ -19,141 +19,141 @@
font-weight: 700;
}
- .terminal-3925029771-matrix {
+ .terminal-3834786767-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3925029771-title {
+ .terminal-3834786767-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
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-.terminal-3925029771-r10 { fill: #8d7b39;font-weight: bold }
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-
+
-
- $ 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 calculate 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-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. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+