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","size"};
commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
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 heatmapArray[] = {"groups","line","label","sorted","scale"};
commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
- string filterseqsArray[] = {"fasta","phylip","clustal","nexus", "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 reverseseqsArray[] = {"fasta"};
+ commandParameters["reverse.seqs"] = addParameters(reverseseqsArray, sizeof(reverseseqsArray)/sizeof(string));
+
+ string trimseqsArray[] = {"fasta", "flip", "oligos"};
+ commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/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 getrepseqsArray[] = {"fasta","line","label","name", "group"};
- commandParameters["get.repseqs"] = addParameters(getrepseqsArray, sizeof(getrepseqsArray)/sizeof(string));
+ string distsharedArray[] = {"line","label","calc","groups"};
+ commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
- string getOTURepArray[] = {"fasta","list","line","label","name"};
+ 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[] = {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
+ string distanceArray[] = {"fasta", "calc", "countends", "cutoff", "processors"};
commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
- string AlignArray[] = {"fasta","phylip","clustal","nexus", "template", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+ string AlignArray[] = {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
string quitArray[] = {};