Changed all mentions of -nc_db and -pt_db to -nc-db and -pt-db in the code

parent 711ab44e
......@@ -90,8 +90,8 @@ void populateParser (Tool *tool) {
tool->getParser()->push_front (new OptionNoParam (STR_SKIP2, "Skips Steps 1 and 2, running only Step 3. Assumes that Steps 1 and 2 were correctly run and folders \"step1\" and \"step2\" are present in the output folder.", false));
tool->getParser()->push_front (new OptionNoParam (STR_SKIP1, "Skips Step 1, running only Steps 2 and 3. Assumes that Step 1 was correctly run and folder \"step1\" is present in the output folder.", false));
tool->getParser()->push_front (new OptionOneParam (STR_OUTPUT, "Path to the folder where the final and temporary files will be stored.", false, "output"));
tool->getParser()->push_front (new OptionOneParam (STR_PROTEIN_DB, "A list of Fasta files separated by comma containing annotations in a protein alphabet format (e.g.: -pt_db path/to/file_1.fa,path/to/file_2.fa,etc). You can customize these files to work better with DBGWAS (see https://gitlab.com/leoisl/dbgwas/tree/master#customizing-annotation-databases).", false));
tool->getParser()->push_front (new OptionOneParam (STR_NUCLEOTIDE_DB, "A list of Fasta files separated by comma containing annotations in a nucleotide alphabet format (e.g.: -nc_db path/to/file_1.fa,path/to/file_2.fa,etc). You can customize these files to work better with DBGWAS (see https://gitlab.com/leoisl/dbgwas/tree/master#customizing-annotation-databases).", false));
tool->getParser()->push_front (new OptionOneParam (STR_PROTEIN_DB, "A list of Fasta files separated by comma containing annotations in a protein alphabet format (e.g.: -pt-db path/to/file_1.fa,path/to/file_2.fa,etc). You can customize these files to work better with DBGWAS (see https://gitlab.com/leoisl/dbgwas/tree/master#customizing-annotation-databases).", false));
tool->getParser()->push_front (new OptionOneParam (STR_NUCLEOTIDE_DB, "A list of Fasta files separated by comma containing annotations in a nucleotide alphabet format (e.g.: -nc-db path/to/file_1.fa,path/to/file_2.fa,etc). You can customize these files to work better with DBGWAS (see https://gitlab.com/leoisl/dbgwas/tree/master#customizing-annotation-databases).", false));
tool->getParser()->push_front (new OptionOneParam (STR_NEWICK_PATH, "Optional path to a newick tree file. If (and only if) a newick tree file is provided, the lineage effect analysis is computed and PCs figures are generated.", false));
tool->getParser()->push_front (new OptionOneParam (STR_KSKMER_SIZE, "K-mer size.", false, "31"));
tool->getParser()->push_front (new OptionOneParam (STR_STRAINS_FILE, "A text file describing the strains containing 3 columns: 1) ID of the strain; 2) Phenotype (0/1/NA); 3) Path to a multi-fasta file containing the sequences of the strain. This file needs a header. Check the sample_example folder or https://gitlab.com/leoisl/dbgwas/raw/master/sample_example/strains for an example.", true));
......
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