//**********************************************************************************************************************
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> SetCurrentCommand::setParameters(){
try {
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pflow);
CommandParameter pfile("file", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfile);
CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pbiom);
CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pphylip);
CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcolumn);
CommandParameter psummary("summary", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psummary);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy);
CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconstaxonomy);
CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcontigsreport);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund);
CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psabund);
CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(porder);
CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptree);
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pshared);
CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pordergroup);
CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount);
CommandParameter pcurrent("current", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcurrent);
CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund);
CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
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, "SetCurrentCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> PipelineCommand::setParameters(){
try {
CommandParameter psff("sff", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(psff);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(poligos);
CommandParameter palign("align", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(palign);
CommandParameter pchimera("chimera", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pchimera);
CommandParameter pclassify("classify", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pclassify);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(ptaxonomy);
CommandParameter ppipeline("pipeline", "InputTypes", "", "", "none", "oneRequired", "none",false,false); parameters.push_back(ppipeline);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
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, "PipelineCommand", "setParameters");
exit(1);
}
}
