Changes

Page history
Update Validate authored by peguerin's avatar peguerin
Show whitespace changes
Inline Side-by-side
Validate.md
View page @ 8962a7b8
......@@ -16,7 +16,7 @@ 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 |
| `--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 |
......@@ -106,7 +106,7 @@ To perform taxonomic assignment in further analysis you need valid FASTA file an
In case the faulty format FASTA file is not empty, you have to correct manually the records in your input FASTA file and run again `mkbdr validate`.
In case the faulty taxonomy FASTA file is not empty, you have to correct the species name of the records in the input FASTA file and run again `mkbdr validate`. You can correct species name manually or use `mkbdr curegen` to generate a curation CSV file that can be use as input of `mkbdr validate --curate` that will apply curation on your input FASTA file.
In case the faulty taxonomy FASTA file is not empty, you have to correct the species name of the records in the input FASTA file and run again `mkbdr validate`. You can correct species name manually or use `mkbdr curegen` (see [Curegen Section](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Curegen) for details) to generate a curation CSV file that can be use as input of `mkbdr validate --curate` that will apply curation on your input FASTA file.
......
......