HelpCommand::HelpCommand(){
globaldata = GlobalData::getInstance();
validCommands = new ValidCommands();
+ validCalcs = new ValidCalculators();
}
//**********************************************************************************************************************
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, order, line and label." << "\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, label=yourLabels)." << "\n";
cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\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 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). " << "\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 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 << "The deconvolute command parameter is fasta and it is required." << "\n";
cout << "The deconvolute command should be in the following format: " << "\n";
cout << "deconvolute(fasta=yourFastaFile) " << "\n";
+ }else if (globaldata->helpRequest == "dist.seqs") {
+ cout << "The dist.seqs command reads a file containing sequences and creates a distance file." << "\n";
+ cout << "The dist.seqs command parameters are fasta, phylip, clustal, nexus, calc, ends, cutoff and processors. " << "\n";
+ cout << "You must use one of the following parameters for your filename: fasta, phylip, clustal or nexus. " << "\n";
+ cout << "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap." << "\n";
+ cout << "The ends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T." << "\n";
+ cout << "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0." << "\n";
+ cout << "The processors parameter allows you to specify number of processors to use. The default is 1, but you can use up to 4 processors." << "\n";
+ cout << "The dist.seqs command should be in the following format: " << "\n";
+ cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, ends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
+ cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, ends=F, cutoff= 2.0, processors=3)." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n";
}else if (globaldata->helpRequest == "collect.single") {
cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";
cout << "The collect.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 collect.single command parameters are label, line, freq, calc. No parameters are required, but you may not use " << "\n";
+ cout << "The collect.single command parameters are label, line, freq, calc and abund. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The collect.single command should be in the following format: " << "\n";
cout << "collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
- cout << "Example collect(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n";
- cout << "The default values for freq is 100, and calc are sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson." << "\n";
+ cout << "Example collect(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n";
+ cout << "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson." << "\n";
+ validCalcs->printCalc("single", cout);
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";
}else if (globaldata->helpRequest == "collect.shared") {
cout << "The collect.shared command can only be executed after a successful read.otu command." << "\n";
- cout << "The collect.shared command parameters are label, line, freq, jumble, calc. No parameters are required, but you may not use " << "\n";
+ cout << "The collect.shared command parameters are label, line, freq, calc and groups. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The collect.shared command should be in the following format: " << "\n";
- cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, jumble=yourJumble, calc=yourEstimators)." << "\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 << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, calc=yourEstimators, groups=yourGroups)." << "\n";
+ cout << "Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
+ cout << "The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ validCalcs->printCalc("shared", cout);
cout << "The label and line parameters are used to analyze specific lines in your input." << "\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 << "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 << "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 << "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 rarefaction.single command parameters are label, line, iters, freq, calc. No parameters are required, but you may not use " << "\n";
+ cout << "The rarefaction.single command parameters are label, line, iters, freq, calc and abund. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The rarefaction.single command should be in the following format: " << "\n";
cout << "rarefaction.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
- cout << "Example rarefaction.single(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson)." << "\n";
+ cout << "Example rarefaction.single(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson)." << "\n";
cout << "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness." << "\n";
+ validCalcs->printCalc("rarefaction", cout);
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";
}else if (globaldata->helpRequest == "rarefaction.shared") {
cout << "The rarefaction.shared command can only be executed after a successful read.otu command." << "\n";
- cout << "The rarefaction.shared command parameters are label, line, iters, jumble and calc. No parameters are required, but you may not use " << "\n";
+ cout << "The rarefaction.shared command parameters are label, line, iters, jumble, groups and calc. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n";
- cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, jumble=yourJumble, calc=yourEstimators)." << "\n";
- cout << "Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000, jumble=1, calc=sharedobserved)." << "\n";
+ cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
+ cout << "Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, jumble=1, groups=B-C, calc=sharedobserved)." << "\n";
cout << "The default values for iters is 1000, jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ validCalcs->printCalc("sharedrarefaction", cout);
cout << "The label and line parameters are used to analyze specific lines in your input." << "\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 << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
}else if (globaldata->helpRequest == "summary.single") {
cout << "The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
cout << "The summary.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 summary.single command parameters are label, line, calc. No parameters are required, but you may not use " << "\n";
+ cout << "The summary.single command parameters are label, line, calc, abund. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n";
cout << "summary.single(label=yourLabel, line=yourLines, calc=yourEstimators)." << "\n";
cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n";
- cout << "The default value calc is sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson" << "\n";
+ validCalcs->printCalc("summary", cout);
+ cout << "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson" << "\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 == "summary.shared") {
cout << "The summary.shared command can only be executed after a successful read.otu command." << "\n";
- cout << "The summary.shared command parameters are label, line, jumble and calc. No parameters are required, but you may not use " << "\n";
+ cout << "The summary.shared command parameters are label, line and calc. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n";
- cout << "summary.shared(label=yourLabel, line=yourLines, jumble=yourJumble, calc=yourEstimators)." << "\n";
- cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
- cout << "The default value for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble) and calc is sharedsobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN" << "\n";
+ cout << "summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups)." << "\n";
+ cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
+ validCalcs->printCalc("sharedsummary", cout);
+ cout << "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan" << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
cout << "The label and line parameters are used to analyze specific lines in your input." << "\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 << "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 default value for groups is all the groups in your groupfile, and iters is 1000." << "\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 == "heatmap") {
+ cout << "The heatmap command can only be executed after a successful read.otu command." << "\n";
+ cout << "The heatmap command parameters are groups, sorted, scale, line and label. No parameters are required, but you may not use line and label at the same time." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
+ cout << "The sorted parameter allows you to choose to see the file with the shared otus at the top or the otus in the order they appear in your input file. " << "\n";
+ cout << "The scale parameter allows you to choose the range of color your bin information will be displayed with." << "\n";
+ cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n";
+ cout << "The heatmap command should be in the following format: heatmap(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example heatmap(groups=A-B-C, line=1-3-5, sorted=F, scale=log10)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
+ cout << "The default value for sorted is T meaning you want the shared otus on top, you may change it to F meaning the exact representation of your input file." << "\n";
+ cout << "The default value for scale is log10; your other options are log2 and linear." << "\n";
+ cout << "The heatmap command outputs a .svg file for each line or label you specify." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "venn") {
+ cout << "The venn command can only be executed after a successful read.otu command." << "\n";
+ cout << "The venn command parameters are groups, calc, line and label. No parameters are required, but you may not use line and label at the same time." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups." << "\n";
+ cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a venn diagram created for, and are also separated by dashes." << "\n";
+ cout << "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile up to 4, and all lines in your inputfile will be used." << "\n";
+ cout << "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups." << "\n";
+ cout << "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file." << "\n";
+ cout << "The only estmiator available four 4 groups is sharedsobs." << "\n";
+ cout << "The venn command outputs a .svg file for each calculator you specify at each distance you choose." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "tree.shared") {
+ cout << "The tree.shared command can only be executed after a successful read.otu command." << "\n";
+ cout << "The tree.shared command parameters are groups, calc, line and label. The calc parameter is required, and you may not use line and label at the same time." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
+ cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
+ cout << "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ cout << "There is no default value for calc." << "\n";
+ validCalcs->printCalc("treegroup", cout);
+ cout << "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "bootstrap.shared") {
+ cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
+ cout << "The bootstrap.shared command parameters are groups, calc, iters, line and label. The calc parameter is required, and you may not use line and label at the same time." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
+ cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
+ cout << "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n";
+ cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ cout << "There is no default value for calc. The default for iters is 1000." << "\n";
+ validCalcs->printCalc("boot", cout);
+ cout << "The bootstrap.shared command outputs a .tre file for each calculator you specify at each distance you choose containing iters number of trees." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "concensus") {
+ cout << "The concensus command can only be executed after a successful read.tree command." << "\n";
+ cout << "The concensus command has no parameters." << "\n";
+ cout << "The concensus command should be in the following format: concensus()." << "\n";
+ cout << "The concensus command output two files: .concensus.tre and .concensuspairs." << "\n";
+ cout << "The .concensus.tre file contains the concensus tree of the trees in your input file." << "\n";
+ cout << "The branch lengths are the percentage of trees in your input file that had the given pair." << "\n";
+ cout << "The .concensuspairs file contains a list of the internal nodes in your tree. For each node, the pair that was used in the concensus tree " << "\n";
+ cout << "is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "bin.seqs") {
+ cout << "The bin.seqs command can only be executed after a successful read.otu command of a list file." << "\n";
+ cout << "The bin.seqs command parameters are fasta, name, line and label. The fasta parameter is required, and you may not use line and label at the same time." << "\n";
+ cout << "The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes." << "\n";
+ cout << "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example bin.seqs(fasta=amazon.fasta, line=1-3-5, name=amazon.names)." << "\n";
+ cout << "The default value for line and label are all lines in your inputfile." << "\n";
+ cout << "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "get.oturep") {
+ cout << "The get.oturep command can only be executed after a successful read.dist command." << "\n";
+ cout << "The get.oturep command parameters are list, fasta, name, line and label. The fasta and list parameters are required, and you may not use line and label at the same time." << "\n";
+ cout << "The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes." << "\n";
+ cout << "The get.oturep command should be in the following format: get.oturep(fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, line=1-3-5, name=amazon.names)." << "\n";
+ cout << "The default value for line and label are all lines in your inputfile." << "\n";
+ cout << "The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\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