#include "makelefsecommand.h"
#include "lefsecommand.h"
#include "kruskalwalliscommand.h"
+#include "sracommand.h"
+#include "mergesfffilecommand.h"
/*******************************************************/
commands["make.lefse"] = "make.lefse";
commands["lefse"] = "lefse";
commands["kruskal.wallis"] = "kruskal.wallis";
+ commands["sra"] = "sra";
+ commands["merge.sfffiles"] = "merge.sfffiles";
}
else { optionString += "inputdir=" + inputDir; }
}
- if(commandName == "cluster") { command = new ClusterCommand(optionString); }
+ if(commandName == "cluster") { command = new ClusterCommand(optionString); }
else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
else if(commandName == "help") { command = new HelpCommand(optionString); }
else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
else if(commandName == "load.logfile") { command = new LoadLogfileCommand(optionString); }
else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
- else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(optionString); }
+ else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(optionString); }
else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
else if(commandName == "make.lefse") { command = new MakeLefseCommand(optionString); }
else if(commandName == "lefse") { command = new LefseCommand(optionString); }
else if(commandName == "kruskal.wallis") { command = new KruskalWallisCommand(optionString); }
+ else if(commandName == "sra") { command = new SRACommand(optionString); }
+ else if(commandName == "merge.sfffiles") { command = new MergeSfffilesCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
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); }
+ else if(commandName == "merge.sfffiles") { pipecommand = new MergeSfffilesCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
else if(commandName == "make.lefse") { shellcommand = new MakeLefseCommand(); }
else if(commandName == "lefse") { shellcommand = new LefseCommand(); }
else if(commandName == "kruskal.wallis") { shellcommand = new KruskalWallisCommand(); }
+ else if(commandName == "sra") { shellcommand = new SRACommand(); }
+ else if(commandName == "merge.sfffiles") { shellcommand = new MergeSfffilesCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;