diff --git a/docs/userguide.rst b/docs/userguide.rst index fb0cc32124f4b3c445aebdd0f69cf8a52fc5d8d4..eef6b43e80d58f4da42e5013665dc890096b2e33 100644 --- a/docs/userguide.rst +++ b/docs/userguide.rst @@ -181,15 +181,15 @@ Here are all available options in **RPG**: **-x, -\\-cleave**: Cleavage site(s) when adding enzyme in non-interactive mode (*e.g.* -x "(D or E,)", similar to -x "(D,)" "(E,)". See :ref:`addenzyme` for more information. -**-z, --exception**: Exception(s) when adding enzyme in non-interactive mode (*e.g.* -z "(D,)(W)" "(D,)(A)". See :ref:`addenzyme` for more information. +**-z, -\\-exception**: Exception(s) when adding enzyme in non-interactive mode (*e.g.* -z "(D,)(W)" "(D,)(A)". See :ref:`addenzyme` for more information. -**-y, --enzname**: Enzyme's name when adding enzyme in non-interactive mode. See :ref:`addenzyme` for more information. +**-y, -\\-enzname**: Enzyme's name when adding enzyme in non-interactive mode. See :ref:`addenzyme` for more information. **-o, -\\-outputfile**: Result file to output resulting peptides (default './peptides.xxx' depending of -\\-fmt). **-p, -\\-pka**: Define pKa values. Either 'ipc2', 'stryer' or 'ipc' (default: ipc2). IPC2 values come from `IPC_peptide in Supplementary Table S1 <https://doi.org/10.1093/nar/gkab295>`_, Stryer values from Biochemistry Stryer, 7th edition and IPC values from `IPC_peptide <http://isoelectric.org/theory.html>`_. -**-w, --mass**: Define atomic mass values. Either 'avg' for average mass or 'mono' for monoisotopic mass. +**-w, -\\-mass**: Define atomic mass values. Either 'avg' for average mass or 'mono' for monoisotopic mass. **-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information.