vector<string> MGClusterCommand::setParameters(){
try {
CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
vector<string> MGClusterCommand::setParameters(){
try {
CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcount);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pcount);
CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }