+ else if(commandName == "deunique.tree") { pipecommand = new DeuniqueTreeCommand(optionString); }
+ else if((commandName == "count.seqs") || (commandName == "make.table")) { pipecommand = new CountSeqsCommand(optionString); }
+ else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(optionString); }
+ else if(commandName == "clear.memory") { pipecommand = new ClearMemoryCommand(optionString); }
+ else if(commandName == "summary.tax") { pipecommand = new SummaryTaxCommand(optionString); }
+ else if(commandName == "summary.qual") { pipecommand = new SummaryQualCommand(optionString); }
+ else if(commandName == "chimera.perseus") { pipecommand = new ChimeraPerseusCommand(optionString); }
+ else if(commandName == "shhh.seqs") { pipecommand = new ShhhSeqsCommand(optionString); }
+ else if(commandName == "otu.association") { pipecommand = new OTUAssociationCommand(optionString); }
+ else if(commandName == "sort.seqs") { pipecommand = new SortSeqsCommand(optionString); }
+ else if(commandName == "classify.tree") { pipecommand = new ClassifyTreeCommand(optionString); }
+ else if(commandName == "cooccurrence") { pipecommand = new CooccurrenceCommand(optionString); }
+ else if(commandName == "pcr.seqs") { pipecommand = new PcrSeqsCommand(optionString); }
+ else if(commandName == "create.database") { pipecommand = new CreateDatabaseCommand(optionString); }
+ else if(commandName == "make.biom") { pipecommand = new MakeBiomCommand(optionString); }
+ else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); }
+ else if(commandName == "list.otulabels") { pipecommand = new ListOtuLabelsCommand(optionString); }
+ else if(commandName == "get.otulabels") { pipecommand = new GetOtuLabelsCommand(optionString); }
+ else if(commandName == "remove.otulabels") { pipecommand = new RemoveOtuLabelsCommand(optionString); }
+ else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
+ else if(commandName == "load.logfile") { pipecommand = new LoadLogfileCommand(optionString); }
+ else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
+ else if(commandName == "classify.rf") { pipecommand = new ClassifyRFSharedCommand(optionString); }
+ else if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
+ else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
+ else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
+ else if(commandName == "remove.dists") { pipecommand = new RemoveDistsCommand(optionString); }
+ else if(commandName == "merge.taxsummary") { pipecommand = new MergeTaxSummaryCommand(optionString); }
+ else if(commandName == "get.communitytype") { pipecommand = new GetMetaCommunityCommand(optionString); }
+ else if(commandName == "sparcc") { pipecommand = new SparccCommand(optionString); }
+ else if(commandName == "make.lookup") { pipecommand = new MakeLookupCommand(optionString); }
+ else if(commandName == "rename.seqs") { pipecommand = new RenameSeqsCommand(optionString); }
+ else if(commandName == "make.lefse") { pipecommand = new MakeLefseCommand(optionString); }
+ else if(commandName == "lefse") { pipecommand = new LefseCommand(optionString); }
+ else if(commandName == "kruskal.wallis") { pipecommand = new KruskalWallisCommand(optionString); }
+ else if(commandName == "sra") { pipecommand = new SRACommand(optionString); }