- cout << "The libshuff command can only be executed after a successful read.dist command including a groupfile." << "\n";
- cout << "The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required." << "\n";
- cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
- cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random matrices you would like compared to your matrix." << "\n";
- cout << "The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form." << "\n";
- cout << "The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete." << "\n";
- cout << "The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep)." << "\n";
- cout << "Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0)." << "\n";
- cout << "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01." << "\n";
- cout << "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters)." << "\n" << "\n";
+ m->mothurOut("The libshuff command can only be executed after a successful read.dist command including a groupfile.\n");
+ m->mothurOut("The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
+ m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random matrices you would like compared to your matrix.\n");
+ m->mothurOut("The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form.\n");
+ m->mothurOut("The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete.\n");
+ m->mothurOut("The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep).\n");
+ m->mothurOut("Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01.\n");
+ m->mothurOut("The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters).\n\n");