cout << "The cluster command should be in the following format: " << "\n";
cout << "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
cout << "The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed." << "\n" << "\n";
- }else if (globaldata->helpRequest == "deconvolute") {
- cout << "The deconvolute command reads a fastafile and creates a namesfile." << "\n";
+ }else if (globaldata->helpRequest == "unique.seqs") {
+ cout << "The unique.seqs command reads a fastafile and creates a namesfile." << "\n";
cout << "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. " << "\n";
cout << "If the sequence is unique the second column will just contain its name. " << "\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";
+ cout << "The unique.seqs command parameter is fasta and it is required." << "\n";
+ cout << "The unique.seqs command should be in the following format: " << "\n";
+ cout << "unique.seqs(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 dist.seqs command parameters are fasta, calc, countends, cutoff and processors. " << "\n";
+ cout << "The fasta parameter is required." << "\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 countends 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 << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
+ cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=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 == "align.seqs") {
cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n";
- cout << "The align.seqs command parameters are fasta, phylip, clustal, nexus, template, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n";
- cout << "You must use one of the following parameters for your candidate filename: fasta, phylip, clustal or nexus. " << "\n";
- cout << "The template parameter is also required." << "\n";
- cout << "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast and distance. The default is suffix." << "\n";
- cout << "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is blast." << "\n";
+ cout << "The align.seqs command parameters are fasta, candidate, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n";
+ cout << "The fasta and candidate parameters are required." << "\n";
+ cout << "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer." << "\n";
+ cout << "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman." << "\n";
cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7." << "\n";
cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n";
cout << "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0." << "\n";
- cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -5.0." << "\n";
+ cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0." << "\n";
cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0." << "\n";
cout << "The align.seqs command should be in the following format: " << "\n";
- cout << "align.seqs(fasta=yourFastaFile, template=yourTemplateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
- cout << "Example align.seqs(fasta=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
+ cout << "align.seqs(fasta=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
+ cout << "Example align.seqs(candidate=candidate.fasta, fasta=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\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 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.group command can only be executed after a successful read.otu command." << "\n";
+//cout << "The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the concensus command." << "\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 << "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";
+ }else if (globaldata->helpRequest == "heatmap.bin") {
+ cout << "The heatmap.bin command can only be executed after a successful read.otu command." << "\n";
+ cout << "The heatmap.bin 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 heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example heatmap.bin(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 << "The heatmap.bin 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 == "heatmap.sim") {
+ cout << "The heatmap.sim command can only be executed after a successful read.otu command." << "\n";
+ cout << "The heatmap.sim 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 heatmap." << "\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.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
+ validCalcs->printCalc("heat", cout);
+ cout << "The default value for calc is jclass-thetayc." << "\n";
+ cout << "The heatmap.sim command outputs a .svg file for each calculator you choose at 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";
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 == "dist.shared") {
+ cout << "The dist.shared command can only be executed after a successful read.otu command." << "\n";
+ cout << "The dist.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 distance matrices created for, and are also separated by dashes." << "\n";
+ cout << "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example dist.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 << "The default value for calc is jclass and thetayc." << "\n";
+ validCalcs->printCalc("matrix", cout);
+ cout << "The dist.shared command outputs a .dist 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 << "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 bin.seqs command parameters are fasta, name, line, label and group. 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 bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, 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 << "If you provide a groupfile, then it also appends the sequences group to the name." << "\n";
cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "filter.seqs") {
+ cout << "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file." << "\n";
+ cout << "The filter.seqs command parameters are fasta, trump, soft, hard and vertical. " << "\n";
+ cout << "The fasta parameter is required." << "\n";
+ cout << "The trump parameter .... The default is ...." << "\n";
+ cout << "The soft parameter .... The default is ...." << "\n";
+ cout << "The hard parameter .... The default is ...." << "\n";
+ cout << "The vertical parameter .... The default is ...." << "\n";
+ cout << "The filter.seqs command should be in the following format: " << "\n";
+ cout << "filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) " << "\n";
+ cout << "Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=...)." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\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 get.oturep command parameters are list, fasta, name, group, 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 get.oturep command should be in the following format: get.oturep(fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups, 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 << "If you provide a groupfile, then it also appends the names of the groups present in that 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 << "The quit command will terminate mothur and should be in the following format: " << "\n";
cout << "quit()" << "\n" << "\n";
}else if (globaldata->helpRequest == "") {
validCommands->printCommands(cout);
projects / mothur.git / blobdiff