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 heatmapArray[] = {"groups","line","label","sorted","scale"};
commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
- string filterseqsArray[] = {"fasta","phylip","clustal","nexus", "trump", "soft", "hard", "vertical"};
+ string filterseqsArray[] = {"fasta", "trump", "soft", "hard", "vertical"};
commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
- string summaryseqsArray[] = {"fasta","phylip","clustal","nexus"};
+ 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 concensusArray[] = {};
commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
- string distanceArray[] = {"fasta","phylip","clustal","nexus", "calc", "countends", "cutoff", "processors"};
+ 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"};