- 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 << "The default value for calc is jclass and thetayc." << "\n";
+ m->mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
+ m->mothurOut("The dist.shared command parameters are groups, calc, output and label. No parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
+ m->mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
+ m->mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
+ m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n");
+ m->mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ m->mothurOut("The default value for calc is jclass and thetayc.\n");