string AmovaCommand::getHelpString(){
try {
string helpString = "";
- helpString += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\n";
- helpString += "The amova command outputs a .amova file. \n";
- helpString += "The amova command parameters are phylip, iters, and alpha. The phylip and design parameters are required, unless you have valid current files.\n";
- helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required. \n";
- helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to.\n";
- helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n";
- helpString += "The amova command should be in the following format: amova(phylip=file.dist, design=file.design).\n";
- helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n\n";
+ helpString += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.";
+ helpString += "The amova command outputs a .amova file.";
+ helpString += "The amova command parameters are phylip, iters, and alpha. The phylip and design parameters are required, unless you have valid current files.";
+ helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required.";
+ helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to.";
+ helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000.";
+ helpString += "The amova command should be in the following format: amova(phylip=file.dist, design=file.design).";
+ helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).";
return helpString;
}
catch(exception& e) {
m->mothurOut("df\t" + toString(dfAmong) + '\t' + toString(dfWithin) + '\t' + toString(dfTotal) + '\n');
AMOVAFile << "MS\t" << MSAmong << '\t' << MSWithin << endl << endl;
- m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n\n");
+ m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n");
AMOVAFile << "Fs:\t" << Fs << endl;
m->mothurOut("Fs:\t" + toString(Fs) + '\n');