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 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 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 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";