int HelpCommand::execute(){
if (globaldata->helpRequest == "read.dist") {
- cout << "The read.dist command parameter options are phylip or column, name, cutoff and precision" << "\n";
- cout << "The read.dist command should be in the following format: " << "\n";
+ cout << "The read.dist command parameter options are phylip or column, group, name, cutoff and precision" << "\n";
+ cout << "The read.dist command must be run before using the cluster or libshuff commands" << "\n";
+ cout << "The read.dist command can be used in two ways. The first is to read a phylip or column and run the cluster command" << "\n";
+ cout << "For this use the read.dist command should be in the following format: " << "\n";
cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
cout << "The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. " << "\n";
cout << "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";
- cout << "Note: No spaces between parameter labels (i.e. dist), '=' and parameters (i.e.yourDistfile)." << "\n" << "\n";
+ cout << "The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command." << "\n";
+ cout << "For this use the read.dist command should be in the following format: " << "\n";
+ cout << "read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. " << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "read.otu") {
cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n";
cout << "collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n";
- cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, group and order." << "\n";
+ cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label." << "\n";
cout << "The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single." << "\n";
- cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile)." << "\n";
+ cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels)." << "\n";
cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
- cout << "The second way to use the read.otu command is to read a list and a group so you can use the collect.shared, rarefaction.shared or summary.shared commands." << "\n";
- cout << "In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile). " << "\n";
- cout << "The list parameter and group paramaters are required. When using the command the second way read.otu command parses the .list file" << "\n";
+ cout << "The line and label parameters are optional but you may not use both the line and label parameters at the same time." << "\n";
+ cout << "The label and line parameters are used to read specific lines in your input." << "\n";
+ cout << "The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands." << "\n";
+ cout << "In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile). " << "\n";
+ cout << "The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file" << "\n";
cout << "and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. " << "\n";
cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "read.tree") {
cout << "The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile)." << "\n";
cout << "The tree and group parameters are both required." << "\n";
cout << "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile)." << "\n" << "\n";
- }else if (globaldata->helpRequest == "read.shared") {
- cout << "The read.shared must be run before you execute a collect.shared, rarefaction.shared or summary.shared command." << "\n";
- cout << "The read.shared command is used to read a shared file. The read.shared should be entered in the following format:" << "\n";
- cout << "read.shared(shared=yourSharedFile). The shared parameter is required." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedfile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "cluster") {
cout << "The cluster command can only be executed after a successful read.dist command." << "\n";
cout << "The cluster command parameter options are method, cuttoff and precision. No parameters are required." << "\n";
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. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\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";
}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 << "The rarefaction.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\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. 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 randomtree parameter." << "\n";
- cout << "The parsimony command parameters are randomtree and iters. No parameters are required." << "\n";
- cout << "The parsimony command should be in the following format: parsimony(randomtree=yourRandomTreeValue, iters=yourIters)." << "\n";
- cout << "Example parsimony(randomtree=1, iters=500)." << "\n";
- cout << "The default value for randomTree is 0 (meaning you want to use the trees in your inputfile, randomtree=1 means you just want the random distribution of trees)," << "\n";
- cout << "and iters is 1000. The parsimony command output three files: .parsimony, .psummary and .pdistrib, their descriptions are in the manual." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
+ 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, 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 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 == "libshuff") {
+ cout << "The libshuff command can only be executed after a successful read.dist command." << "\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";
}else if (globaldata->helpRequest == "quit") {
cout << "The quit command will terminate Dotur and should be in the following format: " << "\n";
cout << "quit()" << "\n" << "\n";
projects / mothur.git / blobdiff