void ClassifySeqsCommand::help(){
try {
mothurOut("The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n");
- mothurOut("The classify.seqs command parameters are template, fasta, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n");
+ mothurOut("The classify.seqs command parameters are template, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n");
mothurOut("The template, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
- mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n");
+ mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast and distance. The default is kmer.\n");
+ mothurOut("The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n");
mothurOut("The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n");
mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
}else{
outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
- cout << classify->getSimpleTax() << endl;
}
outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;