cout << "Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
cout << "The default values for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100 and calc are sharedsobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << "\n";
cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "get.group") {
+ cout << "The get.group command can only be executed after a successful read.otu command of a group file." << "\n";
+ cout << "You may not use any parameters with the get.group command." << "\n";
+ cout << "The get.group command should be in the following format: " << "\n";
+ cout << "get.group()" << "\n";
+ cout << "Example get.group()." << "\n";
+ }else if (globaldata->helpRequest == "get.label") {
+ cout << "The get.label command can only be executed after a successful read.otu command." << "\n";
+ cout << "You may not use any parameters with the get.label command." << "\n";
+ cout << "The get.label command should be in the following format: " << "\n";
+ cout << "get.label()" << "\n";
+ cout << "Example get.label()." << "\n";
+ }else if (globaldata->helpRequest == "get.line") {
+ cout << "The get.line command can only be executed after a successful read.otu command." << "\n";
+ cout << "You may not use any parameters with the get.line command." << "\n";
+ cout << "The get.line command should be in the following format: " << "\n";
+ cout << "get.line()" << "\n";
+ cout << "Example get.line()." << "\n";
cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
}else if (globaldata->helpRequest == "rarefaction.single") {
cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
}else if (globaldata->helpRequest == "parsimony") {
cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter." << "\n";
- cout << "The parsimony command parameters are random and iters. No parameters are required." << "\n";
- cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, iters=yourIters)." << "\n";
+ cout << "The parsimony command parameters are random, groups and iters. 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 1 valid group." << "\n";
+ cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree." << "\n";
+ cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters)." << "\n";
cout << "Example parsimony(random=out, iters=500)." << "\n";
cout << "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony)," << "\n";
- cout << "and iters is 1000. The parsimony command output three files: .parsimony, .psummary and .pdistrib, their descriptions are in the manual." << "\n";
+ cout << "and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual." << "\n";
cout << "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename)." << "\n" << "\n";
}else if (globaldata->helpRequest == "unifrac.weighted") {
cout << "The unifrac.weighted command can only be executed after a successful read.tree command." << "\n";
cout << "The unifrac.weighted command parameters are groups and iters. No parameters are required." << "\n";
- cout << "The groups paramter 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 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 trees you would like compared to your tree." << "\n";
cout << "The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters)." << "\n";
cout << "Example unifrac.weighted(groups=A-B-C, iters=500)." << "\n";
cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n";
- cout << "The unifrac.weighted command output three files: .weighted, .wsummary and .wdistrib, their descriptions are in the manual." << "\n";
+ cout << "The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual." << "\n";
cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "unifrac.unweighted") {
cout << "The unifrac.unweighted command can only be executed after a successful read.tree command." << "\n";
cout << "The unifrac.unweighted command parameters are groups and iters. No parameters are required." << "\n";
- cout << "The groups paramter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group." << "\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 1 valid group." << "\n";
cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree." << "\n";
cout << "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters)." << "\n";
cout << "Example unifrac.unweighted(groups=A-B-C, iters=500)." << "\n";
cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n";
- cout << "The unifrac.unweighted command output three files: .unweighted, .uwsummary and .uwdistrib, their descriptions are in the manual." << "\n";
+ cout << "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual." << "\n";
cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "quit") {
cout << "The quit command will terminate Dotur and should be in the following format: " << "\n";
projects / mothur.git / blobdiff