Validate.md

@@ -17,9 +17,8 @@ This table summarizes the command-line arguments which are using by `mkbdr valid
 | `--fasta` | `-f` | NA | path of the input barcodes sequences FASTA file |
 | `--output_prefix` | `-o` | NA | Output files prefix names |
 | `--curate` | `-c` | NA | path of the input taxonomy curation CSV file. Header must be current_name;ncbi_name;genus;family;ncbi_rank. A curation CSV file can be generated with the command curegen (see the [Curegen section](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Curegen) to learn how to produce a curation file) |
-| `--ncbi_taxdump` | `-n` | NA | path of NCBI taxonomy folder |
-| `--ncbi_taxdump_load` | `-l` | FALSE | load NCBI taxonomy from NCBI taxonomy folder path |
-| `--ncbi_taxdump_edition` | `-e` | FALSE | allow curation to edit NCBI taxonomy files in order to add new taxonomy nodes |
+| `--ncbi_taxdump_load` | `-l` | NA | load NCBI taxonomy archive |
+| `--ncbi_taxonomy_edition` | `-e` | NA | folder of NCBI taxonomy files to edit in order to add new taxonomy nodes |
 
 
 # Example of commands
@@ -61,8 +60,8 @@ 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
+--ncbi_taxdump_load path/to/ncbi_taxo
+
 ```
 
 ete3 will load the files located in `path/to/ncbi_taxo` and stores the NCBI taxonomy tree object in your home folder.
@@ -70,7 +69,7 @@ ete3 will load the files located in `path/to/ncbi_taxo` and stores the NCBI taxo
 
 ### 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).
+* To run mkbdr in order to add new species, you have to allow edition of a given local NCBI taxonomy files with the argument `--ncbi_taxonomy_edition`. 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_.
 
@@ -86,9 +85,7 @@ The MKBDR complete command is:
 mkbdr validate --fasta raw.fasta \
 --output_prefix res \
 --curate curation_new_species.csv \
---ncbi_taxdump path/to/ncbi_taxo \
---ncbi_taxdump_load \
---ncbi_taxdump_edition
+--ncbi_taxonomy_edition path/to/ncbi_taxo
 ```
 
 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`.
@@ -100,7 +97,7 @@ This will edit NCBI taxonomy files located on `path/to/ncbi_taxo` adding  a new
 * Valid FASTA file (see description [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#valid-fasta-file))
 * Faulty taxonomy FASTA file (see description [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#faulty-taxonomy-fasta-file))
 * Faulty format FASTA file (see description [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#faulty-format-fasta-file))
-* Edited taxonomy files: with `--curate`, `--ncbi_taxdump_edition` and `--ncbi_taxdump` options, validate module edits taxonomy files mentionned by `--ncbi_taxdump` so that nodes are added to the tree of life according to curation file specification.
+* Edited taxonomy files: with `--curate` and `--ncbi_taxdump_edition` options, the `validate` module edits taxonomy files located in the folder path given from `--ncbi_taxdump_edition` so that nodes are added to the tree of life according to curation file specification.
 
 To perform taxonomic assignment in further analysis you need valid FASTA file and corresponding taxonomy files.