vector<string> setParameters();
string getCommandName() { return "set.current"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string) { return ""; }
+
string getHelpString();
+ string getOutputPattern(string){ return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
string getDescription() { return "set current files for mothur"; }
string clearTypes;
vector<string> types;
- string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile;
+ string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summaryfile;
string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;