//{"parameter1","parameter2",...,"last parameter"};
string readdistArray[] = {"phylip","column", "name","cutoff","precision", "group"};
-
commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
string readotuArray[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
string readtreeArray[] = {"tree","group"};
commandParameters["read.tree"] = addParameters(readtreeArray, sizeof(readtreeArray)/sizeof(string));
- string readseqsArray[] = {"fasta","phylip","clustal","nexus","line"};
- commandParameters["read.seqs"] = addParameters(readseqsArray, sizeof(readseqsArray)/sizeof(string));
-
string clusterArray[] = {"cutoff","precision","method"};
commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
string deconvoluteArray[] = {"fasta"};
- commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
+ commandParameters["unique.seqs"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
- string collectsingleArray[] = {"freq","line","label","calc","abund"};
+ string collectsingleArray[] = {"freq","line","label","calc","abund","size"};
commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
string collectsharedArray[] = {"freq","line","label","calc","groups"};
string getlineArray[] = {};
commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
+
+ string getsabundArray[] = {"line", "label"};
+ commandParameters["get.sabund"] = addParameters(getsabundArray, sizeof(getsabundArray)/sizeof(string));
+
+ string getrabundArray[] = {"line", "label"};
+ commandParameters["get.rabund"] = addParameters(getrabundArray, sizeof(getrabundArray)/sizeof(string));
string rarefactionsingleArray[] = {"iters","freq","line","label","calc","abund"};
commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
string libshuffArray[] = {"iters","groups","step","form","cutoff"};
commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
- string summarysingleArray[] = {"line","label","calc","abund"};
+ string summarysingleArray[] = {"line","label","calc","abund","size"};
commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
string summarysharedArray[] = {"line","label","calc","groups"};
string heatmapArray[] = {"groups","line","label","sorted","scale"};
commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
- string filterseqsArray[] = {"trump", "soft", "filter"};
+ string filterseqsArray[] = {"fasta", "trump", "soft", "hard", "vertical"};
commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
+ string summaryseqsArray[] = {"fasta"};
+ commandParameters["summary.seqs"] = addParameters(summaryseqsArray, sizeof(summaryseqsArray)/sizeof(string));
+
+ string screenseqsArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
+ commandParameters["screen.seqs"] = addParameters(screenseqsArray, sizeof(screenseqsArray)/sizeof(string));
+
string vennArray[] = {"groups","line","label","calc"};
commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
- string binseqsArray[] = {"fasta","line","label","name"};
+ string binseqsArray[] = {"fasta","line","label","name", "group"};
commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
- string getOTURepArray[] = {"fasta","list","line","label","name"};
+ string distsharedArray[] = {"line","label","calc","groups"};
+ commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
+
+ string getOTURepArray[] = {"fasta","list","line","label","name", "group"};
commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
- string treeGroupsArray[] = {"line","label","calc","groups"};
+ string treeGroupsArray[] = {"line","label","calc","groups", "phylip", "column", "name"};
commandParameters["tree.shared"] = addParameters(treeGroupsArray, sizeof(treeGroupsArray)/sizeof(string));
string bootstrapArray[] = {"line","label","calc","groups","iters"};
string concensusArray[] = {};
commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
- string distanceArray[] = {"calc", "ends", "cutoff", "processors"};
- commandParameters["distance"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+ string distanceArray[] = {"fasta", "calc", "countends", "cutoff", "processors"};
+ commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+
+ string AlignArray[] = {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+ commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
string quitArray[] = {};
commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
string softArray[] = {">=","0", "<=","100", "between"};
parameterRanges["soft"] = addParameters(softArray, rangeSize);
+
+ string sizeArray[] = {">=","1", "<","NA", "between"};
+ parameterRanges["size"] = addParameters(sizeArray, rangeSize);
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";