- 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, shared, group, order, line and label." << "\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, label=yourLabels)." << "\n";
- cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
- cout << "The line and label parameters are optional but you may not use both the line and label parameters at the same time." << "\n";
- cout << "The label and line parameters are used to read specific lines in your input." << "\n";
- cout << "The second way to use the read.otu command is to read a list and a group, or a shared 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, line=yourLines) or read.otu(shared=yourSharedFile). " << "\n";
- cout << "The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file 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";
+ mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
+ mothurOut("collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
+ mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label.\n");
+ mothurOut("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");
+ mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
+ mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
+ mothurOut("The line and label parameters are optional but you may not use both the line and label parameters at the same time.\n");
+ mothurOut("The label and line parameters are used to read specific lines in your input.\n");
+ mothurOut("The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands.\n");
+ mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile). \n");
+ mothurOut("The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file\n");
+ mothurOut("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");
+ mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");