diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg
index 6354851d..ef18862a 100644
--- a/docs/images/sequence-help.svg
+++ b/docs/images/sequence-help.svg
@@ -19,171 +19,171 @@
font-weight: 700;
}
- .terminal-3608076648-matrix {
+ .terminal-3618759029-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3608076648-title {
+ .terminal-3618759029-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
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-
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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 │
-│ 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-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. │
-╰──────────────────────────────────────────────────────────────────────────────╯
-
+
+ $ 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 PATH[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-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. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+
diff --git a/docs/images/train-help.svg b/docs/images/train-help.svg
index 8aab62d4..de672ed2 100644
--- a/docs/images/train-help.svg
+++ b/docs/images/train-help.svg
@@ -19,162 +19,162 @@
font-weight: 700;
}
- .terminal-3079567379-matrix {
+ .terminal-1603172397-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3079567379-title {
+ .terminal-1603172397-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
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-.terminal-3079567379-r9 { fill: #98a84b;font-weight: bold }
-.terminal-3079567379-r10 { fill: #8d7b39;font-weight: bold }
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+.terminal-1603172397-r9 { fill: #98a84b;font-weight: bold }
+.terminal-1603172397-r10 { fill: #8d7b39;font-weight: bold }
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+
@@ -186,53 +186,53 @@
-
+
-
- $ 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-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|er Set the verbosity of │
-│ror] 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. │
-╰──────────────────────────────────────────────────────────────────────────────╯
-
+
+ $ 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 PATH[required]│
+╰──────────────────────────────────────────────────────────────────────────────╯
+╭─ Options ────────────────────────────────────────────────────────────────────╮
+│--validation_peak_path-pPATH 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-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|er Set the verbosity of │
+│ror] 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. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+