cout << "The align.seqs command parameters are fasta, phylip, clustal, nexus, template, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n";
cout << "You must use one of the following parameters for your candidate filename: fasta, phylip, clustal or nexus. " << "\n";
cout << "The template parameter is also required." << "\n";
- cout << "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 suffix." << "\n";
+ cout << "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is suffix." << "\n";
cout << "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is blast." << "\n";
cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7." << "\n";
cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n";
validCalcs->printCalc("treegroup", cout);
cout << "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose." << "\n";
cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "dist.shared") {
+ cout << "The dist.shared command can only be executed after a successful read.otu command." << "\n";
+ cout << "The dist.shared command parameters are groups, calc, line and label. The calc parameter is required, and you may not use line and label at the same time." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
+ cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like distance matrices created for, and are also separated by dashes." << "\n";
+ cout << "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example dist.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ cout << "There is no default value for calc." << "\n";
+ validCalcs->printCalc("matrix", cout);
+ cout << "The dist.shared command outputs a .matrix file for each calculator you specify at each distance you choose." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
}else if (globaldata->helpRequest == "bootstrap.shared") {
cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
cout << "The bootstrap.shared command parameters are groups, calc, iters, line and label. The calc parameter is required, and you may not use line and label at the same time." << "\n";
cout << "The default value for line and label are all lines in your inputfile." << "\n";
cout << "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name." << "\n";
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";
+ cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "get.oturep") {
cout << "The get.oturep command can only be executed after a successful read.dist command." << "\n";
cout << "The get.oturep command parameters are list, fasta, name, line and label. The fasta and list parameters are required, and you may not use line and label at the same time." << "\n";
cout << "The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin." << "\n";
cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "quit") {
- cout << "The quit command will terminate Dotur and should be in the following format: " << "\n";
+ cout << "The quit command will terminate mothur and should be in the following format: " << "\n";
cout << "quit()" << "\n" << "\n";
}else if (globaldata->helpRequest == "") {
validCommands->printCommands(cout);
projects / mothur.git / blobdiff