change -i to -s in user guide when needed

docs/userguide.rst

@@ -115,6 +115,8 @@ To perform sequential digestion of the sequence "QWSDORESDF" with enzymes 2 and
 
     rpg -s QWSDORESDF -o output_file.fasta -e 2 5
 
+.. _onefile:
+
 Sequential digestion of a (multi)fasta file
 """""""""""""""""""""""""""""""""""""""""""
 
@@ -160,7 +162,9 @@ Here are all available options in **RPG**:
 
 **-f, -\\-fmt**: Output file format. Either 'fasta', 'csv', or 'tsv' (default: fasta). See :ref:`formats` for more information.
 
-**-i, -\\-inputdata**: Input file, in (multi)fasta / fastq format or a single protein sequence without commentary. See :ref:`oneseq` for example.
+**-i, -\\-inputdata**: Input file, in (multi)fasta / fastq format. See :ref:`onefile` for example.
+
+**-s, -\\-sequence**:  Input a single protein sequence without commentary. See :ref:`oneseq` for example.
 
 **-l, -\\-list**: Display the list of available enzymes.
 
@@ -268,7 +272,7 @@ Output
 
 Output of **RPG** contains the following information in one line for each generated peptide, in this order:
 
-    - Header of original sequence or 'Input' if the sequence is directly inputed in **RPG**, *i.e.*, **-i** not used with a file
+    - Header of original sequence or 'Input' if the sequence is directly inputed in **RPG**, *i.e.*, **-s**
     - Sequential numbering (starting from 0) of out-coming peptides for each of original sequence
     - Enzyme name used to obtain this peptide
     - Cleavage position on the original sequence (0 if no cleavage occurs)