//**********************************************************************************************************************
vector<string> GetSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "FNGLT", "none","fastq",false,false,true); parameters.push_back(pfastq);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos2);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> SRACommand::setParameters(){
try {
CommandParameter psff("sff", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(psff);
CommandParameter pgroup("group", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(pgroup);
CommandParameter poligos("oligos", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(poligos);
CommandParameter pfile("file", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(pfile);
CommandParameter pfastq("fastq", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(pfastq);
//choose only one multiple options
CommandParameter pplatform("platform", "Multiple", "454-???-???", "454", "", "", "","",false,false); parameters.push_back(pplatform);
CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs);
CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs);
CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
//every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "SRACommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> ListSeqsCommand::setParameters(){
try {
CommandParameter pfastq("fastq", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfastq);
CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(ptaxonomy);
CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false); parameters.push_back(palignreport);
CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "ListSeqsCommand", "setParameters");
exit(1);
}
}