+ 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, 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 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 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 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 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, 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 exact representation of your input file. " << "\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=0)." << "\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 1 meaning you want the shared otus on top, you may change it to 0 meaning the exact representation of your input file." << "\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=yourSorted, 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 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 == "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";