//**********************************************************************************************************************
string MatrixOutputCommand::getHelpString(){
try {
string helpString = "";
ValidCalculators validCalculator;
helpString += "The dist.shared command parameters are shared, groups, calc, output, processors, subsample, iters, mode, and label. shared is a required, unless you have a valid current file.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
helpString += "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";
helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, column and square. The default is lt.\n";
helpString += "The mode parameter allows you to specify if you want the average or the median values reported when subsampling. Options are average, and median. The default is average.\n";
helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
helpString += "The default value for groups is all the groups in your groupfile.\n";
helpString += "The default value for calc is jclass and thetayc.\n";
helpString += validCalculator.printCalc("matrix");
helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n";
helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "MatrixOutputCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string SummarySharedCommand::getHelpString(){
try {
string helpString = "";
ValidCalculators validCalculator;
helpString += "The summary.shared command parameters are shared, label, calc, distance, processors, subsample, iters and all. shared is required if there is no current sharedfile.\n";
helpString += "The summary.shared command should be in the following format: \n";
helpString += "summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n";
helpString += "Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n";
helpString += validCalculator.printCalc("sharedsummary");
helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
helpString += "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n";
helpString += "The default value for groups is all the groups in your groupfile.\n";
helpString += "The distance parameter allows you to indicate you would like a distance file created for each calculator for each label, default=f.\n";
helpString += "The label parameter is used to analyze specific labels in your input.\n";
helpString += "The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n";
helpString += "If you use sharedchao and run into memory issues, set all to false. \n";
helpString += "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";
helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SummarySharedCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string TreeGroupCommand::getHelpString(){
try {
string helpString = "";
ValidCalculators validCalculator;
helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision, processors, subsample, iters and label.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
helpString += "The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n";
helpString += "The phylip or column parameter are required if you do not provide a sharedfile, and only one may be used. If you use a column file the name filename is required. \n";
helpString += "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n";
helpString += "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group. The subsample parameter may only be used with a shared file.\n";
helpString += "Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n";
helpString += "The default value for groups is all the groups in your groupfile.\n";
helpString += "The default value for calc is jclass-thetayc.\n";
helpString += "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n";
helpString += validCalculator.printCalc("treegroup");
helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
helpString += "Example tree.shared(phylip=abrecovery.dist).\n";
helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "TreeGroupCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string RareFactCommand::getHelpString(){
try {
ValidCalculators validCalculator;
string helpString = "";
helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, groupmode, groups, processors and abund. list, sabund, rabund or shared is required unless you have a valid current file. \n";
helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
helpString += "The rarefaction.single command should be in the following format: \n";
helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n";
helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n";
helpString += "The alpha parameter is used to set the alpha value for the shannonrange calculator.\n";
validCalculator.printCalc("rarefaction");
helpString += "If you are running rarefaction.single with a shared file and would like your results collated in one file, set groupmode=t. (Default=true).\n";
helpString += "The label parameter is used to analyze specific labels in your input.\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string SummaryCommand::getHelpString() {
try {
string helpString = "";
ValidCalculators validCalculator;
helpString += "The summary.single command parameters are list, sabund, rabund, shared, subsample, iters, label, calc, abund and groupmode. list, sabund, rabund or shared is required unless you have a valid current file.\n";
helpString += "The summary.single command should be in the following format: \n";
helpString += "summary.single(label=yourLabel, calc=yourEstimators).\n";
helpString += "Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n";
helpString += validCalculator.printCalc("summary");
helpString += "The subsample parameter allows you to enter the size of the sample or you can set subsample=T and mothur will use the size of your smallest group in the case of a shared file. With a list, sabund or rabund file you must provide a subsample size.\n";
helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";
helpString += "If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n";
helpString += "The label parameter is used to analyze specific labels in your input.\n";
helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SummaryCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string CollectSharedCommand::getHelpString(){
try {
string helpString = "";
ValidCalculators validCalculator;
helpString += "The collect.shared command parameters are shared, label, freq, calc and groups. shared is required if there is no current sharedfile. \n";
helpString += "The collect.shared command should be in the following format: \n";
helpString += "collect.shared(label=yourLabel, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n";
helpString += "Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n";
helpString += "The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n";
helpString += "The default value for groups is all the groups in your groupfile.\n";
helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
helpString += validCalculator.printCalc("shared");
helpString += "The label parameter is used to analyze specific labels in your input.\n";
helpString += "The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n";
helpString += "If you use sharedchao and run into memory issues, set all to false. \n";
helpString += "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";
helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "CollectSharedCommand", "getHelpString");
exit(1);
}
}