Validate.md

@@ -10,7 +10,7 @@ The **validate** module produces valid record FASTA file with taxid attributes.
 
 # Command-line Arguments
 
-This table summarizes the command-line arguments which are using by COAT. 
+This table summarizes the command-line arguments which are using by `mkbdr validate`. 
 
 | complete flag argument | short flag | Default value | Summary |
 | --- | --- | --- | --- |
@@ -62,8 +62,6 @@ mkbdr validate --fasta raw.fasta --output_prefix res --curate curation_table.csv
 mkbdr validate --fasta raw.fasta --output_prefix res --ncbi_taxdump path/to/ncbi_taxo --ncbi_taxdump_load
 ```
 
-
-
 ete3 will load the files located in `path/to/ncbi_taxo` and stores the NCBI taxonomy tree object in your home folder. Once the NCBI taxonomy is locally loaded, you can simply run the command:
 
 
@@ -81,6 +79,27 @@ mkbdr validate --fasta raw.fasta --output_prefix res --ncbi_taxdump path/to/an/o
 ```
 
 
+#### Using a local NCBI taxonomy, performs a curation which add new species to your local taxonomy
+
+* To run mkbdr in order to add new species, you have to allow edition of local NCBI taxonomy files with the argument `--ncbi_taxdump_edition`. To specify the location of NCBI taxonomy folder to edit, add the argument `--ncbi_taxdump`. To apply a curation, add the argument `--curate`. Thorough description of curation CSV file is available [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#curation-file).
+
+The following curation CSV gives instruction to MKBDR to create a new custom species called _Distichodus perspicillatus_ with genus _Distichodus_ family _Distichodontidae_.
+
+```
+current_name;ncbi_name;genus;family;ncbi_rank;method
+Distichodus perspicillatus;NA;Distichodus;Distichodontidae;genus;Catalogue of Life
+```
+
+The MKBDR complete command is:
+
+```
+mkbdr validate --fasta raw.fasta --output_prefix res --ncbi_taxdump path/to/ncbi_taxo --ncbi_taxdump_load --ncbi_taxdump_edition
+```
+
+This will edit NCBI taxonomy files located on `path/to/ncbi_taxo` adding  a new custom species  _Distichodus perspicillatus_. This species records will be generated with custom taxid in valid FASTA file output called `res_valid.fasta`.
+
+
+
 # Outputs
 
 * Valid FASTA file (see description [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#valid-fasta-file))