#include "makelefsecommand.h"
#include "lefsecommand.h"
#include "kruskalwalliscommand.h"
+#include "sracommand.h"
/*******************************************************/
commands["make.table"] = "make.table";
commands["sff.multiple"] = "sff.multiple";
commands["quit"] = "MPIEnabled";
- commands["classifyrf.shared"] = "classifyrf.shared";
+ commands["classify.rf"] = "classify.rf";
commands["filter.shared"] = "filter.shared";
commands["primer.design"] = "primer.design";
commands["get.dists"] = "get.dists";
commands["make.lefse"] = "make.lefse";
commands["lefse"] = "lefse";
commands["kruskal.wallis"] = "kruskal.wallis";
+ commands["sra"] = "sra";
}
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 == "classifyrf.shared") { 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 { command = new NoCommand(optionString); }
return command;
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 == "classifyrf.shared") { pipecommand = new ClassifyRFSharedCommand(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 == "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 { pipecommand = new NoCommand(optionString); }
return pipecommand;
else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
else if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); }
else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
- else if(commandName == "classifyrf.shared") { shellcommand = new ClassifyRFSharedCommand(); }
+ else if(commandName == "classify.rf") { shellcommand = new ClassifyRFSharedCommand(); }
else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
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 { shellcommand = new NoCommand(); }
return shellcommand;