- cout << "The read.otu command parameter options are listfile, rabundfile, sabundfile or orderfile." << "\n";
- cout << "The read.otu command should be in the following format: " << "\n";
- cout << "read.otu(listfile=yourListFile, orderfile=yourOrderFile) " << "\n";
- cout << "The read.otu requires one of hte following parameters: listfile, rabundfile or sabundfile. Only one may be used at a time." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
- }else if (globaldata->helpRequest == "read.list") {
- cout << "The read.list command parameter options are listfile and groupfile." << "\n";
- cout << "The read.list command should be in the following format: " << "\n";
- cout << "read.list(listfile=yourListFile, groupfile=yourGroupFile) " << "\n";
- cout << "The listfile parameter and groupfile paramaters are required." << "\n";
- cout << "The read.list command parses a list file and separates it into groups." << "\n";
- cout << "It outputs a .shared file containing the otu information for each group as well as a .list file for each group." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
+ cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n";
+ cout << "collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n";
+ cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, group and order." << "\n";
+ cout << "The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single." << "\n";
+ cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile)." << "\n";
+ cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
+ cout << "The second way to use the read.otu command is to read a list and a group so you can use the collect.shared, rarefaction.shared or summary.shared commands." << "\n";
+ cout << "In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile). " << "\n";
+ cout << "The list parameter and group paramaters are required. When using the command the second way read.otu command parses the .list file" << "\n";
+ cout << "and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. " << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";