- cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
- }else if (globaldata->helpRequest == "get.repseqs") {
- cout << "The get.repseqs command can only be executed after a successful read.otu command of a list file." << "\n";
- cout << "The get.repseqs command parameters are fasta, name, group, line and label. The fasta and group parameters are required, and you may not use line and label at the same time." << "\n";
- cout << "The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes." << "\n";
- cout << "The get.repseqss command should be in the following format: get.repseqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupfile, line=yourLines, label=yourLabels)." << "\n";
- cout << "Example get.repseqs(fasta=amazon.fasta, group=amazon.groups, line=1-3-5, name=amazon.names)." << "\n";
- cout << "The default value for line and label are all lines in your inputfile." << "\n";
- cout << "The get.repseqs command outputs several .fasta files for each distance you specify. " << "\n";
- cout << "If the distance level you choose has bins that contain only sequences unique to a specific group those sequences are outputted to a file for that group." << "\n";
- cout << "If the bin contains sequences from multiple groups then the bin is outputted to the shared fasta file." << "\n";